Ben Bolstad
| Snapshot Date: 2025-11-19 13:40 -0500 (Wed, 19 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: ecdbf23 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-20 11:38 -0500 (Thu, 20 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 251/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.75.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.75.0.tar.gz |
| StartedAt: 2025-11-19 19:53:36 -0500 (Wed, 19 Nov 2025) |
| EndedAt: 2025-11-19 19:54:29 -0500 (Wed, 19 Nov 2025) |
| EllapsedTime: 53.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.75.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.75.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... WARNING
Found the following significant warnings:
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.307 0.143 0.472
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 481268 25.8 1058102 56.6 NA 633897 33.9
Vcells 891509 6.9 8388608 64.0 98304 2110436 16.2
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Wed Nov 19 19:54:02 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Wed Nov 19 19:54:02 2025"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x600002160000>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Wed Nov 19 19:54:07 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Wed Nov 19 19:54:09 2025"
>
> ColMode(tmp2)
<pointer: 0x600002160000>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 97.7572964 -0.7288533 0.2647247 0.7060206
[2,] 1.6891471 -0.4620364 0.1387559 0.4248110
[3,] 0.6882141 0.7594804 -1.5202224 0.9905099
[4,] 1.8994271 -1.3772972 0.8204448 0.4755147
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 97.7572964 0.7288533 0.2647247 0.7060206
[2,] 1.6891471 0.4620364 0.1387559 0.4248110
[3,] 0.6882141 0.7594804 1.5202224 0.9905099
[4,] 1.8994271 1.3772972 0.8204448 0.4755147
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.8872290 0.8537291 0.5145141 0.8402503
[2,] 1.2996719 0.6797326 0.3724995 0.6517753
[3,] 0.8295867 0.8714817 1.2329730 0.9952436
[4,] 1.3781970 1.1735830 0.9057841 0.6895757
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 221.62959 34.26614 30.40987 34.10852
[2,] 39.68587 32.25936 28.86375 31.94256
[3,] 33.98408 34.47430 38.84995 35.94295
[4,] 40.68140 38.11313 34.87829 32.37127
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600002164000>
> exp(tmp5)
<pointer: 0x600002164000>
> log(tmp5,2)
<pointer: 0x600002164000>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 461.2929
> Min(tmp5)
[1] 55.2014
> mean(tmp5)
[1] 72.58322
> Sum(tmp5)
[1] 14516.64
> Var(tmp5)
[1] 818.6919
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.09673 71.28570 72.49345 71.22753 70.15651 70.17339 70.31598 69.65578
[9] 69.53872 69.88843
> rowSums(tmp5)
[1] 1821.935 1425.714 1449.869 1424.551 1403.130 1403.468 1406.320 1393.116
[9] 1390.774 1397.769
> rowVars(tmp5)
[1] 7658.94540 80.63751 58.78153 61.75692 61.26251 89.42533
[7] 39.30308 40.35587 29.35560 46.24704
> rowSd(tmp5)
[1] 87.515401 8.979839 7.666911 7.858557 7.827037 9.456497 6.269217
[8] 6.352627 5.418080 6.800518
> rowMax(tmp5)
[1] 461.29295 87.92740 82.27819 84.78726 84.60307 92.39995 82.70521
[8] 85.46396 78.66847 82.37886
> rowMin(tmp5)
[1] 55.20140 59.06968 55.70316 58.59725 59.15106 56.63472 56.48290 61.21111
[9] 58.72507 57.29928
>
> colMeans(tmp5)
[1] 110.89942 69.03638 68.17052 74.97340 67.32642 67.72802 71.08531
[8] 71.65383 67.77595 66.40594 74.82565 71.89097 73.55525 69.84339
[15] 69.58143 71.87790 68.46555 71.11585 71.16809 74.28517
> colSums(tmp5)
[1] 1108.9942 690.3638 681.7052 749.7340 673.2642 677.2802 710.8531
[8] 716.5383 677.7595 664.0594 748.2565 718.9097 735.5525 698.4339
[15] 695.8143 718.7790 684.6555 711.1585 711.6809 742.8517
> colVars(tmp5)
[1] 15219.69718 59.50275 44.27853 49.38772 43.38334 33.47798
[7] 48.63209 88.44696 91.47148 22.74585 13.85463 20.65234
[13] 74.57719 69.18683 45.14111 69.14636 68.75696 67.70886
[19] 23.35762 94.38825
> colSd(tmp5)
[1] 123.368137 7.713803 6.654212 7.027640 6.586603 5.786016
[7] 6.973671 9.404625 9.564073 4.769261 3.722180 4.544485
[13] 8.635809 8.317862 6.718713 8.315429 8.291982 8.228539
[19] 4.832972 9.715361
> colMax(tmp5)
[1] 461.29295 79.32748 80.86109 85.46396 78.09765 77.08984 82.56139
[8] 87.92079 84.78726 73.79644 79.20473 80.22345 84.60307 87.92740
[15] 81.17518 82.40259 78.84326 82.70521 76.39075 92.39995
> colMin(tmp5)
[1] 60.72302 56.63472 58.72507 66.48426 59.15106 58.82656 61.70901 62.75664
[9] 55.70316 58.29727 68.77876 66.60775 58.59725 58.82841 59.76770 56.48290
[17] 55.20140 59.94745 60.07362 59.06968
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 91.09673 71.28570 72.49345 71.22753 70.15651 70.17339 70.31598 69.65578
[9] NA 69.88843
> rowSums(tmp5)
[1] 1821.935 1425.714 1449.869 1424.551 1403.130 1403.468 1406.320 1393.116
[9] NA 1397.769
> rowVars(tmp5)
[1] 7658.94540 80.63751 58.78153 61.75692 61.26251 89.42533
[7] 39.30308 40.35587 30.71758 46.24704
> rowSd(tmp5)
[1] 87.515401 8.979839 7.666911 7.858557 7.827037 9.456497 6.269217
[8] 6.352627 5.542344 6.800518
> rowMax(tmp5)
[1] 461.29295 87.92740 82.27819 84.78726 84.60307 92.39995 82.70521
[8] 85.46396 NA 82.37886
> rowMin(tmp5)
[1] 55.20140 59.06968 55.70316 58.59725 59.15106 56.63472 56.48290 61.21111
[9] NA 57.29928
>
> colMeans(tmp5)
[1] 110.89942 69.03638 68.17052 74.97340 67.32642 67.72802 71.08531
[8] 71.65383 67.77595 66.40594 74.82565 71.89097 73.55525 69.84339
[15] 69.58143 71.87790 68.46555 NA 71.16809 74.28517
> colSums(tmp5)
[1] 1108.9942 690.3638 681.7052 749.7340 673.2642 677.2802 710.8531
[8] 716.5383 677.7595 664.0594 748.2565 718.9097 735.5525 698.4339
[15] 695.8143 718.7790 684.6555 NA 711.6809 742.8517
> colVars(tmp5)
[1] 15219.69718 59.50275 44.27853 49.38772 43.38334 33.47798
[7] 48.63209 88.44696 91.47148 22.74585 13.85463 20.65234
[13] 74.57719 69.18683 45.14111 69.14636 68.75696 NA
[19] 23.35762 94.38825
> colSd(tmp5)
[1] 123.368137 7.713803 6.654212 7.027640 6.586603 5.786016
[7] 6.973671 9.404625 9.564073 4.769261 3.722180 4.544485
[13] 8.635809 8.317862 6.718713 8.315429 8.291982 NA
[19] 4.832972 9.715361
> colMax(tmp5)
[1] 461.29295 79.32748 80.86109 85.46396 78.09765 77.08984 82.56139
[8] 87.92079 84.78726 73.79644 79.20473 80.22345 84.60307 87.92740
[15] 81.17518 82.40259 78.84326 NA 76.39075 92.39995
> colMin(tmp5)
[1] 60.72302 56.63472 58.72507 66.48426 59.15106 58.82656 61.70901 62.75664
[9] 55.70316 58.29727 68.77876 66.60775 58.59725 58.82841 59.76770 56.48290
[17] 55.20140 NA 60.07362 59.06968
>
> Max(tmp5,na.rm=TRUE)
[1] 461.2929
> Min(tmp5,na.rm=TRUE)
[1] 55.2014
> mean(tmp5,na.rm=TRUE)
[1] 72.6093
> Sum(tmp5,na.rm=TRUE)
[1] 14449.25
> Var(tmp5,na.rm=TRUE)
[1] 822.69
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.09673 71.28570 72.49345 71.22753 70.15651 70.17339 70.31598 69.65578
[9] 69.65157 69.88843
> rowSums(tmp5,na.rm=TRUE)
[1] 1821.935 1425.714 1449.869 1424.551 1403.130 1403.468 1406.320 1393.116
[9] 1323.380 1397.769
> rowVars(tmp5,na.rm=TRUE)
[1] 7658.94540 80.63751 58.78153 61.75692 61.26251 89.42533
[7] 39.30308 40.35587 30.71758 46.24704
> rowSd(tmp5,na.rm=TRUE)
[1] 87.515401 8.979839 7.666911 7.858557 7.827037 9.456497 6.269217
[8] 6.352627 5.542344 6.800518
> rowMax(tmp5,na.rm=TRUE)
[1] 461.29295 87.92740 82.27819 84.78726 84.60307 92.39995 82.70521
[8] 85.46396 78.66847 82.37886
> rowMin(tmp5,na.rm=TRUE)
[1] 55.20140 59.06968 55.70316 58.59725 59.15106 56.63472 56.48290 61.21111
[9] 58.72507 57.29928
>
> colMeans(tmp5,na.rm=TRUE)
[1] 110.89942 69.03638 68.17052 74.97340 67.32642 67.72802 71.08531
[8] 71.65383 67.77595 66.40594 74.82565 71.89097 73.55525 69.84339
[15] 69.58143 71.87790 68.46555 71.52934 71.16809 74.28517
> colSums(tmp5,na.rm=TRUE)
[1] 1108.9942 690.3638 681.7052 749.7340 673.2642 677.2802 710.8531
[8] 716.5383 677.7595 664.0594 748.2565 718.9097 735.5525 698.4339
[15] 695.8143 718.7790 684.6555 643.7640 711.6809 742.8517
> colVars(tmp5,na.rm=TRUE)
[1] 15219.69718 59.50275 44.27853 49.38772 43.38334 33.47798
[7] 48.63209 88.44696 91.47148 22.74585 13.85463 20.65234
[13] 74.57719 69.18683 45.14111 69.14636 68.75696 74.24903
[19] 23.35762 94.38825
> colSd(tmp5,na.rm=TRUE)
[1] 123.368137 7.713803 6.654212 7.027640 6.586603 5.786016
[7] 6.973671 9.404625 9.564073 4.769261 3.722180 4.544485
[13] 8.635809 8.317862 6.718713 8.315429 8.291982 8.616787
[19] 4.832972 9.715361
> colMax(tmp5,na.rm=TRUE)
[1] 461.29295 79.32748 80.86109 85.46396 78.09765 77.08984 82.56139
[8] 87.92079 84.78726 73.79644 79.20473 80.22345 84.60307 87.92740
[15] 81.17518 82.40259 78.84326 82.70521 76.39075 92.39995
> colMin(tmp5,na.rm=TRUE)
[1] 60.72302 56.63472 58.72507 66.48426 59.15106 58.82656 61.70901 62.75664
[9] 55.70316 58.29727 68.77876 66.60775 58.59725 58.82841 59.76770 56.48290
[17] 55.20140 59.94745 60.07362 59.06968
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.09673 71.28570 72.49345 71.22753 70.15651 70.17339 70.31598 69.65578
[9] NaN 69.88843
> rowSums(tmp5,na.rm=TRUE)
[1] 1821.935 1425.714 1449.869 1424.551 1403.130 1403.468 1406.320 1393.116
[9] 0.000 1397.769
> rowVars(tmp5,na.rm=TRUE)
[1] 7658.94540 80.63751 58.78153 61.75692 61.26251 89.42533
[7] 39.30308 40.35587 NA 46.24704
> rowSd(tmp5,na.rm=TRUE)
[1] 87.515401 8.979839 7.666911 7.858557 7.827037 9.456497 6.269217
[8] 6.352627 NA 6.800518
> rowMax(tmp5,na.rm=TRUE)
[1] 461.29295 87.92740 82.27819 84.78726 84.60307 92.39995 82.70521
[8] 85.46396 NA 82.37886
> rowMin(tmp5,na.rm=TRUE)
[1] 55.20140 59.06968 55.70316 58.59725 59.15106 56.63472 56.48290 61.21111
[9] NA 57.29928
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.48063 69.35289 69.22001 74.79658 66.82655 67.90253 70.99508
[8] 72.32665 67.64136 67.17290 74.57896 72.41836 74.53818 69.53844
[15] 69.15870 71.85745 68.43660 NaN 71.50387 74.15494
> colSums(tmp5,na.rm=TRUE)
[1] 1030.3257 624.1760 622.9801 673.1692 601.4390 611.1227 638.9557
[8] 650.9398 608.7722 604.5561 671.2107 651.7653 670.8436 625.8460
[15] 622.4283 646.7170 615.9294 0.0000 643.5348 667.3944
> colVars(tmp5,na.rm=TRUE)
[1] 16977.87685 65.81356 37.42217 55.20943 45.99523 37.32015
[7] 54.61951 94.41019 102.70161 18.97144 14.90185 20.10485
[13] 73.03004 76.78902 48.77341 77.78495 77.34215 NA
[19] 25.00891 105.99595
> colSd(tmp5,na.rm=TRUE)
[1] 130.299182 8.112556 6.117366 7.430305 6.781978 6.109022
[7] 7.390502 9.716491 10.134180 4.355622 3.860291 4.483843
[13] 8.545762 8.762934 6.983796 8.819578 8.794439 NA
[19] 5.000891 10.295434
> colMax(tmp5,na.rm=TRUE)
[1] 461.29295 79.32748 80.86109 85.46396 78.09765 77.08984 82.56139
[8] 87.92079 84.78726 73.79644 79.20473 80.22345 84.60307 87.92740
[15] 81.17518 82.40259 78.84326 -Inf 76.39075 92.39995
> colMin(tmp5,na.rm=TRUE)
[1] 60.72302 56.63472 60.07612 66.48426 59.15106 58.82656 61.70901 62.75664
[9] 55.70316 58.29727 68.77876 66.60775 58.59725 58.82841 59.76770 56.48290
[17] 55.20140 Inf 60.07362 59.06968
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 99.22438 349.46171 391.25024 298.13252 173.48121 257.28707 290.60799
[8] 303.32217 262.35492 210.80930
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 99.22438 349.46171 391.25024 298.13252 173.48121 257.28707 290.60799
[8] 303.32217 262.35492 210.80930
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 5.684342e-14 -8.526513e-14 -1.136868e-13 5.684342e-14 5.684342e-14
[6] 1.136868e-13 -5.684342e-14 -5.684342e-14 0.000000e+00 -5.684342e-14
[11] -1.705303e-13 0.000000e+00 -3.979039e-13 1.136868e-13 -1.705303e-13
[16] -1.989520e-13 0.000000e+00 1.136868e-13 2.842171e-14 5.684342e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
5 2
1 3
9 2
5 7
9 15
5 2
7 12
5 7
8 1
4 20
3 10
8 18
10 9
2 15
7 10
2 3
2 18
3 10
4 6
9 10
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.24674
> Min(tmp)
[1] -2.474682
> mean(tmp)
[1] -0.07885375
> Sum(tmp)
[1] -7.885375
> Var(tmp)
[1] 1.108306
>
> rowMeans(tmp)
[1] -0.07885375
> rowSums(tmp)
[1] -7.885375
> rowVars(tmp)
[1] 1.108306
> rowSd(tmp)
[1] 1.052761
> rowMax(tmp)
[1] 2.24674
> rowMin(tmp)
[1] -2.474682
>
> colMeans(tmp)
[1] -0.40991503 -0.79076537 -0.64182470 -0.98517631 0.87569083 0.59551011
[7] -0.21405050 -0.10314158 0.16970880 -0.69793499 1.67098615 -0.31270624
[13] -0.15716505 0.29353903 -1.81898581 -2.39345372 -0.87032231 -0.22684827
[19] -0.52424525 1.59448739 -1.00766699 2.20772078 0.69805850 -0.33773172
[25] -1.83489037 -0.58843811 -2.47468153 0.87890561 1.19629172 -0.89221660
[31] 1.89423810 0.57739653 -1.32854500 -0.23871876 -0.03890046 -1.17062073
[37] -1.87534137 -0.39276851 -0.51871569 -0.66996733 1.25805416 -0.52463495
[43] -0.33609212 0.34077435 0.05522570 0.44683878 -0.54414478 -0.58104597
[49] 1.93818250 0.28928644 0.54274696 1.76625795 0.40429242 -0.20172275
[55] -0.82830584 1.13930773 2.24673974 0.05725367 0.28090584 -0.21880385
[61] -1.35274417 0.79739388 0.15230522 -0.31474616 -0.45220090 -0.19038679
[67] -0.72305343 -1.28709358 0.39167140 0.29371034 0.32610758 -2.42382159
[73] -0.31892745 -0.83371585 0.50050685 -0.93196898 1.40404325 -0.98070519
[79] 1.13139787 -1.93084465 1.00299869 -0.08124647 1.03727115 0.33554643
[85] 0.83120722 -0.30748815 -0.23687011 -1.26809044 -1.50085212 1.65464699
[91] 0.31629504 1.94412451 0.93339988 0.28353390 0.65375123 -0.55091125
[97] 0.67683666 -1.08323840 -0.35701704 -2.09411128
> colSums(tmp)
[1] -0.40991503 -0.79076537 -0.64182470 -0.98517631 0.87569083 0.59551011
[7] -0.21405050 -0.10314158 0.16970880 -0.69793499 1.67098615 -0.31270624
[13] -0.15716505 0.29353903 -1.81898581 -2.39345372 -0.87032231 -0.22684827
[19] -0.52424525 1.59448739 -1.00766699 2.20772078 0.69805850 -0.33773172
[25] -1.83489037 -0.58843811 -2.47468153 0.87890561 1.19629172 -0.89221660
[31] 1.89423810 0.57739653 -1.32854500 -0.23871876 -0.03890046 -1.17062073
[37] -1.87534137 -0.39276851 -0.51871569 -0.66996733 1.25805416 -0.52463495
[43] -0.33609212 0.34077435 0.05522570 0.44683878 -0.54414478 -0.58104597
[49] 1.93818250 0.28928644 0.54274696 1.76625795 0.40429242 -0.20172275
[55] -0.82830584 1.13930773 2.24673974 0.05725367 0.28090584 -0.21880385
[61] -1.35274417 0.79739388 0.15230522 -0.31474616 -0.45220090 -0.19038679
[67] -0.72305343 -1.28709358 0.39167140 0.29371034 0.32610758 -2.42382159
[73] -0.31892745 -0.83371585 0.50050685 -0.93196898 1.40404325 -0.98070519
[79] 1.13139787 -1.93084465 1.00299869 -0.08124647 1.03727115 0.33554643
[85] 0.83120722 -0.30748815 -0.23687011 -1.26809044 -1.50085212 1.65464699
[91] 0.31629504 1.94412451 0.93339988 0.28353390 0.65375123 -0.55091125
[97] 0.67683666 -1.08323840 -0.35701704 -2.09411128
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -0.40991503 -0.79076537 -0.64182470 -0.98517631 0.87569083 0.59551011
[7] -0.21405050 -0.10314158 0.16970880 -0.69793499 1.67098615 -0.31270624
[13] -0.15716505 0.29353903 -1.81898581 -2.39345372 -0.87032231 -0.22684827
[19] -0.52424525 1.59448739 -1.00766699 2.20772078 0.69805850 -0.33773172
[25] -1.83489037 -0.58843811 -2.47468153 0.87890561 1.19629172 -0.89221660
[31] 1.89423810 0.57739653 -1.32854500 -0.23871876 -0.03890046 -1.17062073
[37] -1.87534137 -0.39276851 -0.51871569 -0.66996733 1.25805416 -0.52463495
[43] -0.33609212 0.34077435 0.05522570 0.44683878 -0.54414478 -0.58104597
[49] 1.93818250 0.28928644 0.54274696 1.76625795 0.40429242 -0.20172275
[55] -0.82830584 1.13930773 2.24673974 0.05725367 0.28090584 -0.21880385
[61] -1.35274417 0.79739388 0.15230522 -0.31474616 -0.45220090 -0.19038679
[67] -0.72305343 -1.28709358 0.39167140 0.29371034 0.32610758 -2.42382159
[73] -0.31892745 -0.83371585 0.50050685 -0.93196898 1.40404325 -0.98070519
[79] 1.13139787 -1.93084465 1.00299869 -0.08124647 1.03727115 0.33554643
[85] 0.83120722 -0.30748815 -0.23687011 -1.26809044 -1.50085212 1.65464699
[91] 0.31629504 1.94412451 0.93339988 0.28353390 0.65375123 -0.55091125
[97] 0.67683666 -1.08323840 -0.35701704 -2.09411128
> colMin(tmp)
[1] -0.40991503 -0.79076537 -0.64182470 -0.98517631 0.87569083 0.59551011
[7] -0.21405050 -0.10314158 0.16970880 -0.69793499 1.67098615 -0.31270624
[13] -0.15716505 0.29353903 -1.81898581 -2.39345372 -0.87032231 -0.22684827
[19] -0.52424525 1.59448739 -1.00766699 2.20772078 0.69805850 -0.33773172
[25] -1.83489037 -0.58843811 -2.47468153 0.87890561 1.19629172 -0.89221660
[31] 1.89423810 0.57739653 -1.32854500 -0.23871876 -0.03890046 -1.17062073
[37] -1.87534137 -0.39276851 -0.51871569 -0.66996733 1.25805416 -0.52463495
[43] -0.33609212 0.34077435 0.05522570 0.44683878 -0.54414478 -0.58104597
[49] 1.93818250 0.28928644 0.54274696 1.76625795 0.40429242 -0.20172275
[55] -0.82830584 1.13930773 2.24673974 0.05725367 0.28090584 -0.21880385
[61] -1.35274417 0.79739388 0.15230522 -0.31474616 -0.45220090 -0.19038679
[67] -0.72305343 -1.28709358 0.39167140 0.29371034 0.32610758 -2.42382159
[73] -0.31892745 -0.83371585 0.50050685 -0.93196898 1.40404325 -0.98070519
[79] 1.13139787 -1.93084465 1.00299869 -0.08124647 1.03727115 0.33554643
[85] 0.83120722 -0.30748815 -0.23687011 -1.26809044 -1.50085212 1.65464699
[91] 0.31629504 1.94412451 0.93339988 0.28353390 0.65375123 -0.55091125
[97] 0.67683666 -1.08323840 -0.35701704 -2.09411128
> colMedians(tmp)
[1] -0.40991503 -0.79076537 -0.64182470 -0.98517631 0.87569083 0.59551011
[7] -0.21405050 -0.10314158 0.16970880 -0.69793499 1.67098615 -0.31270624
[13] -0.15716505 0.29353903 -1.81898581 -2.39345372 -0.87032231 -0.22684827
[19] -0.52424525 1.59448739 -1.00766699 2.20772078 0.69805850 -0.33773172
[25] -1.83489037 -0.58843811 -2.47468153 0.87890561 1.19629172 -0.89221660
[31] 1.89423810 0.57739653 -1.32854500 -0.23871876 -0.03890046 -1.17062073
[37] -1.87534137 -0.39276851 -0.51871569 -0.66996733 1.25805416 -0.52463495
[43] -0.33609212 0.34077435 0.05522570 0.44683878 -0.54414478 -0.58104597
[49] 1.93818250 0.28928644 0.54274696 1.76625795 0.40429242 -0.20172275
[55] -0.82830584 1.13930773 2.24673974 0.05725367 0.28090584 -0.21880385
[61] -1.35274417 0.79739388 0.15230522 -0.31474616 -0.45220090 -0.19038679
[67] -0.72305343 -1.28709358 0.39167140 0.29371034 0.32610758 -2.42382159
[73] -0.31892745 -0.83371585 0.50050685 -0.93196898 1.40404325 -0.98070519
[79] 1.13139787 -1.93084465 1.00299869 -0.08124647 1.03727115 0.33554643
[85] 0.83120722 -0.30748815 -0.23687011 -1.26809044 -1.50085212 1.65464699
[91] 0.31629504 1.94412451 0.93339988 0.28353390 0.65375123 -0.55091125
[97] 0.67683666 -1.08323840 -0.35701704 -2.09411128
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.409915 -0.7907654 -0.6418247 -0.9851763 0.8756908 0.5955101 -0.2140505
[2,] -0.409915 -0.7907654 -0.6418247 -0.9851763 0.8756908 0.5955101 -0.2140505
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.1031416 0.1697088 -0.697935 1.670986 -0.3127062 -0.1571651 0.293539
[2,] -0.1031416 0.1697088 -0.697935 1.670986 -0.3127062 -0.1571651 0.293539
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.818986 -2.393454 -0.8703223 -0.2268483 -0.5242453 1.594487 -1.007667
[2,] -1.818986 -2.393454 -0.8703223 -0.2268483 -0.5242453 1.594487 -1.007667
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 2.207721 0.6980585 -0.3377317 -1.83489 -0.5884381 -2.474682 0.8789056
[2,] 2.207721 0.6980585 -0.3377317 -1.83489 -0.5884381 -2.474682 0.8789056
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.196292 -0.8922166 1.894238 0.5773965 -1.328545 -0.2387188 -0.03890046
[2,] 1.196292 -0.8922166 1.894238 0.5773965 -1.328545 -0.2387188 -0.03890046
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.170621 -1.875341 -0.3927685 -0.5187157 -0.6699673 1.258054 -0.524635
[2,] -1.170621 -1.875341 -0.3927685 -0.5187157 -0.6699673 1.258054 -0.524635
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.3360921 0.3407743 0.0552257 0.4468388 -0.5441448 -0.581046 1.938182
[2,] -0.3360921 0.3407743 0.0552257 0.4468388 -0.5441448 -0.581046 1.938182
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.2892864 0.542747 1.766258 0.4042924 -0.2017228 -0.8283058 1.139308
[2,] 0.2892864 0.542747 1.766258 0.4042924 -0.2017228 -0.8283058 1.139308
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 2.24674 0.05725367 0.2809058 -0.2188039 -1.352744 0.7973939 0.1523052
[2,] 2.24674 0.05725367 0.2809058 -0.2188039 -1.352744 0.7973939 0.1523052
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.3147462 -0.4522009 -0.1903868 -0.7230534 -1.287094 0.3916714 0.2937103
[2,] -0.3147462 -0.4522009 -0.1903868 -0.7230534 -1.287094 0.3916714 0.2937103
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.3261076 -2.423822 -0.3189275 -0.8337158 0.5005069 -0.931969 1.404043
[2,] 0.3261076 -2.423822 -0.3189275 -0.8337158 0.5005069 -0.931969 1.404043
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.9807052 1.131398 -1.930845 1.002999 -0.08124647 1.037271 0.3355464
[2,] -0.9807052 1.131398 -1.930845 1.002999 -0.08124647 1.037271 0.3355464
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.8312072 -0.3074881 -0.2368701 -1.26809 -1.500852 1.654647 0.316295
[2,] 0.8312072 -0.3074881 -0.2368701 -1.26809 -1.500852 1.654647 0.316295
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 1.944125 0.9333999 0.2835339 0.6537512 -0.5509112 0.6768367 -1.083238
[2,] 1.944125 0.9333999 0.2835339 0.6537512 -0.5509112 0.6768367 -1.083238
[,99] [,100]
[1,] -0.357017 -2.094111
[2,] -0.357017 -2.094111
>
>
> Max(tmp2)
[1] 3.338279
> Min(tmp2)
[1] -2.831849
> mean(tmp2)
[1] -0.03405012
> Sum(tmp2)
[1] -3.405012
> Var(tmp2)
[1] 1.064644
>
> rowMeans(tmp2)
[1] 0.99676215 0.36505481 0.59501246 -0.25022086 0.63461315 -0.40567528
[7] 0.29058244 -0.63434886 0.88741749 1.31087815 -2.83184929 -1.06281743
[13] 0.19859185 1.16224568 0.30558725 -1.40856092 0.85463803 0.34827742
[19] -1.09963348 1.01170254 0.49892660 -0.10677244 -1.49243802 0.28376495
[25] -1.43543713 0.46050449 -1.07674920 0.01707330 0.24627101 -0.78016442
[31] -1.97996576 -0.01246025 0.81627628 -1.13265481 0.36470150 0.37601714
[37] 0.48534075 -0.98787235 -0.13820151 -1.07552187 -0.17420664 -1.06525113
[43] -0.17158311 1.61162110 2.17712535 -1.74975095 -0.44551412 0.04365382
[49] 0.36906349 0.10034288 0.99372101 -1.75915548 -0.42245530 -1.57221626
[55] -1.58803332 0.90026324 -0.91597757 -0.59663199 -0.29280950 -0.95702349
[61] 0.07183570 1.84524052 1.09009875 -0.29423460 0.06205911 -1.02165274
[67] -0.67015612 -0.13036509 1.76090782 -0.08844627 -0.93197134 0.07447136
[73] 0.53535402 0.90294939 -2.71354399 -0.01186078 0.91704521 -0.80976937
[79] 0.03376434 -0.80676109 1.30438241 -1.52869149 0.07991169 0.43117338
[85] -0.54964918 -0.04609882 -0.87127698 0.45466860 0.66275478 0.06585766
[91] 0.67001537 0.59946935 0.53231904 1.51548386 -0.98796952 -0.13489728
[97] 3.33827918 -0.22786835 0.93065400 1.45742746
> rowSums(tmp2)
[1] 0.99676215 0.36505481 0.59501246 -0.25022086 0.63461315 -0.40567528
[7] 0.29058244 -0.63434886 0.88741749 1.31087815 -2.83184929 -1.06281743
[13] 0.19859185 1.16224568 0.30558725 -1.40856092 0.85463803 0.34827742
[19] -1.09963348 1.01170254 0.49892660 -0.10677244 -1.49243802 0.28376495
[25] -1.43543713 0.46050449 -1.07674920 0.01707330 0.24627101 -0.78016442
[31] -1.97996576 -0.01246025 0.81627628 -1.13265481 0.36470150 0.37601714
[37] 0.48534075 -0.98787235 -0.13820151 -1.07552187 -0.17420664 -1.06525113
[43] -0.17158311 1.61162110 2.17712535 -1.74975095 -0.44551412 0.04365382
[49] 0.36906349 0.10034288 0.99372101 -1.75915548 -0.42245530 -1.57221626
[55] -1.58803332 0.90026324 -0.91597757 -0.59663199 -0.29280950 -0.95702349
[61] 0.07183570 1.84524052 1.09009875 -0.29423460 0.06205911 -1.02165274
[67] -0.67015612 -0.13036509 1.76090782 -0.08844627 -0.93197134 0.07447136
[73] 0.53535402 0.90294939 -2.71354399 -0.01186078 0.91704521 -0.80976937
[79] 0.03376434 -0.80676109 1.30438241 -1.52869149 0.07991169 0.43117338
[85] -0.54964918 -0.04609882 -0.87127698 0.45466860 0.66275478 0.06585766
[91] 0.67001537 0.59946935 0.53231904 1.51548386 -0.98796952 -0.13489728
[97] 3.33827918 -0.22786835 0.93065400 1.45742746
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 0.99676215 0.36505481 0.59501246 -0.25022086 0.63461315 -0.40567528
[7] 0.29058244 -0.63434886 0.88741749 1.31087815 -2.83184929 -1.06281743
[13] 0.19859185 1.16224568 0.30558725 -1.40856092 0.85463803 0.34827742
[19] -1.09963348 1.01170254 0.49892660 -0.10677244 -1.49243802 0.28376495
[25] -1.43543713 0.46050449 -1.07674920 0.01707330 0.24627101 -0.78016442
[31] -1.97996576 -0.01246025 0.81627628 -1.13265481 0.36470150 0.37601714
[37] 0.48534075 -0.98787235 -0.13820151 -1.07552187 -0.17420664 -1.06525113
[43] -0.17158311 1.61162110 2.17712535 -1.74975095 -0.44551412 0.04365382
[49] 0.36906349 0.10034288 0.99372101 -1.75915548 -0.42245530 -1.57221626
[55] -1.58803332 0.90026324 -0.91597757 -0.59663199 -0.29280950 -0.95702349
[61] 0.07183570 1.84524052 1.09009875 -0.29423460 0.06205911 -1.02165274
[67] -0.67015612 -0.13036509 1.76090782 -0.08844627 -0.93197134 0.07447136
[73] 0.53535402 0.90294939 -2.71354399 -0.01186078 0.91704521 -0.80976937
[79] 0.03376434 -0.80676109 1.30438241 -1.52869149 0.07991169 0.43117338
[85] -0.54964918 -0.04609882 -0.87127698 0.45466860 0.66275478 0.06585766
[91] 0.67001537 0.59946935 0.53231904 1.51548386 -0.98796952 -0.13489728
[97] 3.33827918 -0.22786835 0.93065400 1.45742746
> rowMin(tmp2)
[1] 0.99676215 0.36505481 0.59501246 -0.25022086 0.63461315 -0.40567528
[7] 0.29058244 -0.63434886 0.88741749 1.31087815 -2.83184929 -1.06281743
[13] 0.19859185 1.16224568 0.30558725 -1.40856092 0.85463803 0.34827742
[19] -1.09963348 1.01170254 0.49892660 -0.10677244 -1.49243802 0.28376495
[25] -1.43543713 0.46050449 -1.07674920 0.01707330 0.24627101 -0.78016442
[31] -1.97996576 -0.01246025 0.81627628 -1.13265481 0.36470150 0.37601714
[37] 0.48534075 -0.98787235 -0.13820151 -1.07552187 -0.17420664 -1.06525113
[43] -0.17158311 1.61162110 2.17712535 -1.74975095 -0.44551412 0.04365382
[49] 0.36906349 0.10034288 0.99372101 -1.75915548 -0.42245530 -1.57221626
[55] -1.58803332 0.90026324 -0.91597757 -0.59663199 -0.29280950 -0.95702349
[61] 0.07183570 1.84524052 1.09009875 -0.29423460 0.06205911 -1.02165274
[67] -0.67015612 -0.13036509 1.76090782 -0.08844627 -0.93197134 0.07447136
[73] 0.53535402 0.90294939 -2.71354399 -0.01186078 0.91704521 -0.80976937
[79] 0.03376434 -0.80676109 1.30438241 -1.52869149 0.07991169 0.43117338
[85] -0.54964918 -0.04609882 -0.87127698 0.45466860 0.66275478 0.06585766
[91] 0.67001537 0.59946935 0.53231904 1.51548386 -0.98796952 -0.13489728
[97] 3.33827918 -0.22786835 0.93065400 1.45742746
>
> colMeans(tmp2)
[1] -0.03405012
> colSums(tmp2)
[1] -3.405012
> colVars(tmp2)
[1] 1.064644
> colSd(tmp2)
[1] 1.031816
> colMax(tmp2)
[1] 3.338279
> colMin(tmp2)
[1] -2.831849
> colMedians(tmp2)
[1] 0.03870908
> colRanges(tmp2)
[,1]
[1,] -2.831849
[2,] 3.338279
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.7092789 0.5356221 1.9161059 1.9649762 5.0109287 -1.4313218
[7] -2.2562957 3.8543905 2.1281324 4.1009564
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.7125305
[2,] -0.7894352
[3,] -0.2281121
[4,] 0.3597437
[5,] 0.9168152
>
> rowApply(tmp,sum)
[1] -0.8754725 -3.4720272 -0.1506065 0.1481318 4.3806115 4.0984134
[7] 5.9141150 4.5109251 -2.5337529 1.0938783
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 10 8 4 4 3 1 2 8 1
[2,] 5 3 5 7 6 5 8 3 5 7
[3,] 8 5 9 2 5 6 9 7 1 4
[4,] 10 2 2 9 10 2 6 6 2 10
[5,] 7 9 7 6 3 8 4 10 6 3
[6,] 3 7 3 8 1 10 2 1 10 2
[7,] 6 1 6 1 7 1 5 8 4 6
[8,] 9 4 1 5 9 9 10 5 3 8
[9,] 4 8 4 10 2 4 7 4 9 9
[10,] 2 6 10 3 8 7 3 9 7 5
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 3.174913613 -2.451345524 1.870491820 1.575974148 -3.696832049
[6] -0.600493775 -2.956243311 1.390780774 -1.501948014 0.824912982
[11] 1.679812239 -1.382224051 -0.642638149 -3.039195442 2.999446620
[16] 0.008111706 2.275516462 -0.560464742 6.918991879 1.251859324
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.9508162
[2,] -0.3287499
[3,] 1.0377847
[4,] 1.2920862
[5,] 2.1246088
>
> rowApply(tmp,sum)
[1] 9.7976960 0.8018752 -2.2825335 3.2303389 -4.4079501
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 15 17 20 8 5
[2,] 19 1 3 9 4
[3,] 3 11 11 17 17
[4,] 10 14 14 3 20
[5,] 2 4 4 2 18
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.0377847 1.6185536 -0.304474171 0.4748330 -0.8897718 -1.6384189
[2,] 1.2920862 -1.4196446 0.319636620 0.9510389 -1.1925612 -0.6172384
[3,] 2.1246088 -1.3631044 0.002419048 0.2122806 -0.8563750 1.6360504
[4,] -0.3287499 -0.3256863 1.189383023 -1.5496927 -1.6878591 -0.6142619
[5,] -0.9508162 -0.9614638 0.663527300 1.4875143 0.9297350 0.6333750
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.5887815 1.2732928 0.3436928 -0.04107889 0.2545514 -0.1455291
[2,] -1.3827798 1.5465413 0.6222944 0.03315408 1.0454577 -0.7624787
[3,] -0.1930957 0.4489035 -1.5208470 -0.14012890 -0.8319033 -0.8065112
[4,] -0.7164960 -0.5739488 -0.5889854 2.52502127 0.8821214 0.8824225
[5,] -1.2526533 -1.3040080 -0.3581028 -1.55205459 0.3295850 -0.5501276
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.842573748 1.0790818 -0.2075385 -0.04700879 1.4978069 0.84938301
[2,] -1.393802083 -1.1334166 0.4220528 -0.70392001 0.9869421 -1.07852676
[3,] 0.004926923 -0.5045758 1.2066591 0.41202281 -0.5790821 0.06767126
[4,] 0.335181504 -1.9914865 2.0037713 1.00528015 -0.1546893 0.18541790
[5,] -0.431518241 -0.4887983 -0.4254981 -0.65826245 0.5245388 -0.58441014
[,19] [,20]
[1,] 2.7245201 0.4866606
[2,] 1.9709831 1.2960562
[3,] 0.7240726 -2.3265252
[4,] 0.4796387 2.2739571
[5,] 1.0197773 -0.4782893
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 650 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 563 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 1.19235 -2.852936 -1.826968 -0.4599499 1.865361 -0.1664343 -1.638237
col8 col9 col10 col11 col12 col13 col14
row1 1.248158 -0.139359 0.5598795 0.3851552 -0.08337798 -0.5930323 -0.1998345
col15 col16 col17 col18 col19 col20
row1 -1.212385 -0.1274342 -1.396042 1.31041 -0.1224624 -2.00825
> tmp[,"col10"]
col10
row1 0.55987945
row2 0.09075196
row3 -2.09942539
row4 -0.31048452
row5 1.73046598
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 1.1923495 -2.852936 -1.8269678 -0.45994989 1.865361 -0.1664343 -1.638237
row5 -0.2159416 1.585593 -0.4016775 -0.04811175 1.476905 1.1966698 1.209086
col8 col9 col10 col11 col12 col13
row1 1.2481576 -0.1393590 0.5598795 0.3851552 -0.08337798 -0.5930323
row5 -0.9281624 0.6079036 1.7304660 -1.5806442 -0.14850706 -2.4249828
col14 col15 col16 col17 col18 col19 col20
row1 -0.1998345 -1.212385 -0.1274342 -1.396042 1.310410 -0.1224624 -2.0082503
row5 -0.2047116 -1.651912 1.6885733 0.179165 -1.308275 -1.1300546 0.7366072
> tmp[,c("col6","col20")]
col6 col20
row1 -0.1664343 -2.0082503
row2 -1.2293937 0.1549297
row3 0.9013852 1.0028716
row4 -0.2069002 -0.8026183
row5 1.1966698 0.7366072
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.1664343 -2.0082503
row5 1.1966698 0.7366072
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.54032 49.07791 50.87543 49.78494 50.90061 103.9442 50.7303 47.82678
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.01364 49.23193 49.25403 50.94446 49.61858 49.92179 50.92923 51.3361
col17 col18 col19 col20
row1 50.14199 49.56951 50.13419 105.7536
> tmp[,"col10"]
col10
row1 49.23193
row2 28.68119
row3 28.99215
row4 28.84277
row5 50.33064
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.54032 49.07791 50.87543 49.78494 50.90061 103.9442 50.73030 47.82678
row5 50.70932 49.15251 51.75500 48.92814 49.40605 105.1273 48.41732 49.45637
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.01364 49.23193 49.25403 50.94446 49.61858 49.92179 50.92923 51.3361
row5 51.86723 50.33064 50.98268 50.29992 48.95121 49.47082 50.09468 48.7797
col17 col18 col19 col20
row1 50.14199 49.56951 50.13419 105.7536
row5 49.58688 51.02006 49.69201 106.4331
> tmp[,c("col6","col20")]
col6 col20
row1 103.94423 105.75356
row2 75.01510 75.41991
row3 75.03377 74.05267
row4 74.79262 74.29028
row5 105.12725 106.43310
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.9442 105.7536
row5 105.1273 106.4331
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.9442 105.7536
row5 105.1273 106.4331
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -1.1672137
[2,] 0.4701690
[3,] 0.2233076
[4,] 0.5399296
[5,] 1.2362392
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.24084061 -0.2845619
[2,] 0.08248523 -2.3713876
[3,] -0.56118377 1.0151584
[4,] -1.90727561 1.7709291
[5,] 0.72932466 -0.7778369
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.9050257 -1.36579952
[2,] -1.0381368 0.57295991
[3,] 1.0450112 -0.40288307
[4,] 0.6445822 -0.68037586
[5,] 0.4658239 -0.08736485
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.9050257
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.9050257
[2,] -1.0381368
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 1.1374509 0.6660118 1.542145 -0.07594575 0.6008276 0.8897145 -0.5105099
row1 0.3610142 2.0470765 -1.253453 0.44054875 0.2415474 -2.2314808 -1.1209521
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.06801526 0.6684780 -0.2598513 0.1141884 -0.7956300 1.1690501
row1 -0.66817415 -0.9482665 -0.4079967 -0.4494692 -0.3602558 0.7187741
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.1011883 -0.9475555 0.3673362 -2.147702 0.6250473 -1.1320912 1.9127700
row1 -0.8345033 -0.1360282 0.6125809 1.455285 -0.1246100 0.5210582 0.7898719
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.02880511 -0.849695 -0.374648 0.269599 0.908441 0.411153 0.8715537
[,8] [,9] [,10]
row2 0.2675033 0.2229686 -0.6308537
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.5764115 -0.01559314 -1.36731 0.4287258 -0.901254 -0.1586832 0.4360446
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.1748621 2.446965 0.09547752 0.2253556 -0.06518135 -0.1990241 -2.315376
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.107599 -0.601185 -1.25026 0.395754 1.144974 0.06954973
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x600002148000>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa301f4eca2d"
[2] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa3017dbb5834"
[3] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa301169bfe69"
[4] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa3015b5bab17"
[5] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa3015f3da1dc"
[6] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa301474da35d"
[7] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa3013a20533d"
[8] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa3012038e79b"
[9] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa30177ed81a3"
[10] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa3019da31d8"
[11] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa30153fe60f5"
[12] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa301618f9fe7"
[13] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa3011c4b28bb"
[14] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa301a5f1b80"
[15] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BMa3016a0675d1"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x60000212c0c0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x60000212c0c0>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x60000212c0c0>
> rowMedians(tmp)
[1] 0.4518930901 0.1068390774 0.0208903257 -0.2486192365 0.4222483890
[6] -0.1754838674 -0.0705389895 0.3855424391 -0.4363085739 0.2798886553
[11] 0.7134647011 0.2475201918 -0.2039106323 -0.3885633062 -0.3857905449
[16] -0.0577395430 -0.4219214575 -0.2699827398 0.1238876431 -0.1694286118
[21] 0.0985975418 0.2066744275 0.1518844877 -0.1650436390 0.2843594188
[26] 0.6690906049 -0.6376201660 0.2790484379 -0.5479560603 0.1102122986
[31] -0.1382970855 0.3820271627 -0.0556255183 0.1295651344 0.1754580670
[36] -0.2575379146 0.2815710087 -0.0331050041 -0.1617623893 0.1443125963
[41] -0.2552653485 -0.2278613876 0.1719316458 0.0007193052 -0.1735252247
[46] -0.8393300590 -0.1020565772 0.2425446266 0.1638250144 0.4467318079
[51] 0.0400071543 -0.4320099616 -0.0167256323 -0.1743182687 -0.6232502138
[56] 0.0340225873 -0.2208574620 -0.0298183540 -0.1147034110 -0.6419942682
[61] 0.1149670393 -0.5430313075 0.2678917453 0.2214055311 -0.1226335332
[66] -0.0682016003 -0.4895036937 0.1796417659 -0.2297458996 0.0500630108
[71] -0.2031834621 -0.3271846533 -0.1192565039 -0.0236490730 -0.2070645829
[76] 0.2570531511 -0.0434474350 -0.7226269556 -0.2597690672 0.1308214553
[81] -0.0809842203 -0.3193835333 -0.1992471396 0.2072299913 0.4859104046
[86] 0.1651478081 -0.2251191486 0.1930962066 -0.2500858784 -0.4600932523
[91] 0.4576438123 -0.3976885608 -0.0898476679 0.0648276315 -0.2113610538
[96] 0.6147914509 0.0013562710 -0.0758233276 0.0600616759 1.1944812226
[101] -0.3655185990 -0.2587523569 0.3928863190 -0.1266938482 0.1204282780
[106] -0.3642006789 -0.2932056633 -0.0832401658 0.3356511683 0.0764656347
[111] 0.2740709981 -0.0774144895 -0.2725436413 0.0511873939 0.2251007031
[116] -0.0158410609 0.0263046212 0.4524175625 0.0210101339 -0.7162496460
[121] -0.3829181311 0.2435679774 0.0230818096 -0.0866248572 -0.3503392333
[126] 0.3394338643 -0.1032009783 0.0172206771 -1.0787805902 0.1354741923
[131] 0.3095208547 -0.0138364692 0.4389553501 -0.3154142860 0.0323919371
[136] -0.0123263432 -0.0898630979 0.4720231259 -0.5932548426 -0.0992233303
[141] 0.5205647212 -0.1722990528 -0.1426611645 0.6079531562 0.0306333802
[146] -0.5816175692 -0.1019451974 0.4169475925 -0.0346144436 -0.2435106113
[151] -0.6761104087 -0.3292210509 -0.5788487610 -0.3231861707 0.5827616590
[156] 0.1136128647 0.0605995155 0.7088676939 0.3743367827 0.1872951610
[161] -0.0016060000 -0.4612111171 0.1518500911 -0.1842097652 -0.0986924110
[166] 0.1940260956 -0.3259598521 -0.3286358615 0.0301661812 -0.2883275329
[171] 0.0959884065 0.4757496983 -0.2270056367 -0.3871161849 0.3388936348
[176] -0.2527309552 0.3448893858 -0.1600395835 -0.1254916974 0.4952285500
[181] -0.1722615979 -0.1368887692 0.2025603937 -0.0897886082 0.0819748062
[186] 0.5342368477 0.5196439341 -0.0556899742 -0.6016335720 -0.2690587881
[191] 0.4262455005 -0.3316977375 -0.0637124935 0.2336907661 -0.4542752219
[196] -0.3560519203 0.0079852362 0.0222172976 -0.3201215151 -0.1285749816
[201] -0.1529297886 -0.5228518086 0.0499876436 -0.0577714912 0.6461741041
[206] -0.4805276851 -0.1518442041 -0.0692648748 0.2487354243 0.0824461068
[211] 0.4127536847 -0.6905129611 0.2985009861 -0.2530503044 0.2141569064
[216] 0.1305747438 -0.2457489750 0.3696553022 0.3395691685 -0.0798009220
[221] -0.2134168098 0.3699381504 0.0346905730 -0.1013310747 -0.6672602624
[226] -0.3817994919 0.0423950576 -0.5218452129 0.3581781068 0.2184947414
>
> proc.time()
user system elapsed
2.669 14.987 18.306
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600002ae4180>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600002ae4180>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600002ae4180>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x600002ae4180>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x600002aa8000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002aa8000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x600002aa8000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002aa8000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600002aa8000>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002ae00c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002ae00c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600002ae00c0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600002ae00c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600002ae00c0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600002ae00c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600002ae00c0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600002ae00c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600002ae00c0>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002aa0000>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600002aa0000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002aa0000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002aa0000>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilea935490bdad5" "BufferedMatrixFilea9357dd2a6b"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilea935490bdad5" "BufferedMatrixFilea9357dd2a6b"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002aa0240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002aa0240>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600002aa0240>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600002aa0240>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x600002aa0240>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x600002aa0240>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002aa0420>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002aa0420>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600002aa0420>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x600002aa0420>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600002aa04e0>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600002aa04e0>
> rm(P)
>
> proc.time()
user system elapsed
0.321 0.152 0.488
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
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Platform: x86_64-apple-darwin20
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.315 0.095 0.445