Charlotte Soneson
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/compcodeR |
| Branch: RELEASE_3_12 |
| Last Commit: b692f6a |
| Last Changed Date: 2020-11-08 11:24:58 -0400 (Sun, 08 Nov 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:36 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the compcodeR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 359/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compcodeR 1.26.1 (landing page) Charlotte Soneson
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: compcodeR |
| Version: 1.26.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.26.1.tar.gz |
| StartedAt: 2021-05-06 00:32:48 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:38:59 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 371.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: compcodeR.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.26.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/compcodeR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compcodeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compcodeR’ version ‘1.26.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rpanel’
* 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 ‘compcodeR’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/compcodeR.Rcheck/00install.out’ for details.
* 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 R 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 ... NOTE
'library' or 'require' call to ‘rpanel’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘sm’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NBPSeq.createRmd 36.953 1.074 38.114
DESeq2.createRmd 23.909 2.871 26.671
NOISeq.prenorm.createRmd 10.758 8.737 18.763
EBSeq.createRmd 9.015 0.888 9.907
show-compData-method 7.150 0.956 8.031
DSS.createRmd 6.916 0.998 7.896
convertcompDataToList 6.495 0.972 7.423
baySeq.createRmd 5.731 0.964 6.681
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/compcodeR.Rcheck/00check.log’
for details.
compcodeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL compcodeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘compcodeR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’ ** testing if installed package keeps a record of temporary installation path * DONE (compcodeR)
compcodeR.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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(testthat)
> library(compcodeR)
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Warning message:
replacing previous import 'gdata::reorder.factor' by 'gplots::reorder.factor' when loading 'compcodeR'
>
> test_check("compcodeR")
ordinary text without R code
label: settings (with options)
List of 1
$ echo: logi FALSE
label: modifications (with options)
List of 1
$ echo: logi FALSE
label: calcma (with options)
List of 4
$ echo : logi FALSE
$ dev : chr "png"
$ eval : logi TRUE
$ include: logi TRUE
ordinary text without R code
label: maplot-trueDEstatus (with options)
List of 7
$ echo : logi FALSE
$ dev : chr "png"
$ eval : logi TRUE
$ include: logi TRUE
$ message: logi FALSE
$ error : logi TRUE
$ warning: logi TRUE
ordinary text without R code
label: maplot-nbroutliers (with options)
List of 7
$ echo : logi FALSE
$ dev : chr "png"
$ eval : logi TRUE
$ include: logi TRUE
$ message: logi FALSE
$ error : logi TRUE
$ warning: logi TRUE
ordinary text without R code
label: logfoldchanges (with options)
List of 7
$ echo : logi FALSE
$ dev : chr "png"
$ eval : logi TRUE
$ include: logi TRUE
$ message: logi FALSE
$ error : logi TRUE
$ warning: logi TRUE
[1] "DESeq2.createRmd" "DSS.createRmd"
[3] "EBSeq.createRmd" "NBPSeq.createRmd"
[5] "NOISeq.prenorm.createRmd" "TCC.createRmd"
[7] "baySeq.createRmd" "edgeR.GLM.createRmd"
[9] "edgeR.exact.createRmd" "logcpm.limma.createRmd"
[11] "sqrtcpm.limma.createRmd" "ttest.createRmd"
[13] "voom.limma.createRmd" "voom.ttest.createRmd"
ordinary text without R code
label: unnamed-chunk-1 (with options)
List of 6
$ echo : logi TRUE
$ eval : logi TRUE
$ include: logi TRUE
$ message: logi TRUE
$ error : logi TRUE
$ warning: logi TRUE
ordinary text without R code
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An object of class compData
Dataset name: B_625_625
Number of samples: 10
Number of variables: 500
Number of random outliers: 0
Number of single outliers: 0
Number of known truly differentially expressed genes: 50
Differential expression analysis was performed by the method EBSeq.1.30.0.median on Thu May 6 00:38:23 2021 .
count.matrix:
sample1 sample2 sample3 sample4 sample5 sample6
g1 4 8 5 2 8 8
g2 314 419 186 172 294 133
g3 1030 1583 1011 1033 747 1291
g4 0 1 1 0 2 2
g5 48 122 215 62 106 90
g6 27 16 18 44 29 74
+ 494 rows and 4 cols...
sample.annotations:
condition depth.factor
sample1 1 1.1049378
sample2 1 1.2875127
sample3 1 1.1581115
sample4 1 1.3611698
sample5 1 1.0581603
sample6 2 0.7594447
+ 4 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.11610054 0.11610054 6.878049 16.363472
g2 0.43796296 0.43796296 303.073171 893.165617
g3 0.04321133 0.04321133 1223.414634 2760.990905
g4 0.55624371 0.55624371 0.902439 6.153083
g5 0.15968189 0.15968189 148.146341 316.915193
g6 0.36378999 0.36378999 40.439024 132.785087
n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.single.outliers.down.S1 n.single.outliers.down.S2 M.value A.value
g1 0 0 1.158386 2.9291506
g2 0 0 1.349570 8.6365105
g3 0 0 1.050582 10.4859190
g4 0 0 1.432447 0.7393097
g5 0 0 1.185233 7.1150497
g6 0 0 2.176450 5.6916570
truelog2foldchanges upregulation downregulation differential.expression
g1 1.250408 1 0 1
g2 1.559262 1 0 1
g3 1.174273 1 0 1
g4 2.769408 1 0 1
g5 1.097074 1 0 1
g6 1.715273 1 0 1
+ 494 rows...
Differential expression results:
FDR lfdr score posterior.DE
g1 9.063873e-01 1.000000e+00 0.0936127 3.618046e-19
g2 2.191315e-01 6.800099e-01 0.7808685 3.199901e-01
g3 7.537978e-04 2.194364e-03 0.9992462 9.978056e-01
g4 3.164914e-01 7.574579e-01 0.6835086 2.425421e-01
g5 2.900704e-01 7.294102e-01 0.7099296 2.705898e-01
g6 3.802565e-06 1.288441e-05 0.9999962 9.999871e-01
+ 494 rows...
An object of class compData
Dataset name: B_625_625
Number of samples: 4
Number of variables: 500
Number of random outliers: 0
Number of single outliers: 0
Number of known truly differentially expressed genes: 50
Differential expression analysis was performed by the method EBSeq.1.30.0.median on Thu May 6 00:38:23 2021 .
count.matrix:
sample1 sample2 sample3 sample4
g1 4 8 5 2
g2 314 419 186 172
g3 1030 1583 1011 1033
g4 0 1 1 0
g5 48 122 215 62
g6 27 16 18 44
+ 494 rows...
sample.annotations:
condition depth.factor
sample1 1 1.1049378
sample2 1 1.2875127
sample3 1 1.1581115
sample4 1 1.3611698
sample5 1 1.0581603
sample6 2 0.7594447
+ 4 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.11610054 0.11610054 6.878049 16.363472
g2 0.43796296 0.43796296 303.073171 893.165617
g3 0.04321133 0.04321133 1223.414634 2760.990905
g4 0.55624371 0.55624371 0.902439 6.153083
g5 0.15968189 0.15968189 148.146341 316.915193
g6 0.36378999 0.36378999 40.439024 132.785087
n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.single.outliers.down.S1 n.single.outliers.down.S2 M.value A.value
g1 0 0 1.158386 2.9291506
g2 0 0 1.349570 8.6365105
g3 0 0 1.050582 10.4859190
g4 0 0 1.432447 0.7393097
g5 0 0 1.185233 7.1150497
g6 0 0 2.176450 5.6916570
truelog2foldchanges upregulation downregulation differential.expression
g1 1.250408 1 0 1
g2 1.559262 1 0 1
g3 1.174273 1 0 1
g4 2.769408 1 0 1
g5 1.097074 1 0 1
g6 1.715273 1 0 1
+ 494 rows...
Differential expression results:
FDR lfdr score posterior.DE
g1 9.063873e-01 1.000000e+00 0.0936127 3.618046e-19
g2 2.191315e-01 6.800099e-01 0.7808685 3.199901e-01
g3 7.537978e-04 2.194364e-03 0.9992462 9.978056e-01
g4 3.164914e-01 7.574579e-01 0.6835086 2.425421e-01
g5 2.900704e-01 7.294102e-01 0.7099296 2.705898e-01
g6 3.802565e-06 1.288441e-05 0.9999962 9.999871e-01
+ 494 rows...
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 285 ]
>
> proc.time()
user system elapsed
103.412 14.476 117.172
compcodeR.Rcheck/compcodeR-Ex.timings
| name | user | system | elapsed | |
| DESeq2.createRmd | 23.909 | 2.871 | 26.671 | |
| DSS.createRmd | 6.916 | 0.998 | 7.896 | |
| EBSeq.createRmd | 9.015 | 0.888 | 9.907 | |
| NBPSeq.createRmd | 36.953 | 1.074 | 38.114 | |
| NOISeq.prenorm.createRmd | 10.758 | 8.737 | 18.763 | |
| TCC.createRmd | 3.207 | 0.433 | 3.650 | |
| baySeq.createRmd | 5.731 | 0.964 | 6.681 | |
| checkDataObject | 0.511 | 0.093 | 0.600 | |
| checkTableConsistency | 1.669 | 0.227 | 1.917 | |
| check_compData | 0.559 | 0.085 | 0.639 | |
| check_compData_results | 1.111 | 0.159 | 1.263 | |
| compData | 0.002 | 0.000 | 0.003 | |
| convertListTocompData | 0.005 | 0.002 | 0.007 | |
| convertcompDataToList | 6.495 | 0.972 | 7.423 | |
| edgeR.GLM.createRmd | 1.596 | 0.199 | 1.787 | |
| edgeR.exact.createRmd | 1.179 | 0.159 | 1.340 | |
| generateCodeHTMLs | 1.093 | 0.150 | 1.237 | |
| generateSyntheticData | 0.588 | 0.085 | 0.667 | |
| listcreateRmd | 0.013 | 0.000 | 0.014 | |
| logcpm.limma.createRmd | 0.937 | 0.137 | 1.064 | |
| runComparison | 1.743 | 0.202 | 1.933 | |
| runComparisonGUI | 0.001 | 0.000 | 0.002 | |
| runDiffExp | 1.120 | 0.146 | 1.256 | |
| show-compData-method | 7.150 | 0.956 | 8.031 | |
| sqrtcpm.limma.createRmd | 0.899 | 0.135 | 1.025 | |
| summarizeSyntheticDataSet | 0.582 | 0.086 | 0.661 | |
| ttest.createRmd | 0.933 | 0.136 | 1.060 | |
| voom.limma.createRmd | 1.028 | 0.145 | 1.171 | |
| voom.ttest.createRmd | 0.879 | 0.138 | 1.013 | |