David Montaner
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/mdgsa |
| Branch: RELEASE_3_7 |
| Last Commit: 57c1d96 |
| Last Changed Date: 2018-05-23 09:24:11 -0400 (Wed, 23 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:39:46 -0400 (Wed, 17 Oct 2018).
| Package 850/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mdgsa 1.12.1 David Montaner
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: mdgsa |
| Version: 1.12.1 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mdgsa.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings mdgsa_1.12.1.tar.gz |
| StartedAt: 2018-10-17 03:07:26 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:10:12 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 166.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mdgsa.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mdgsa.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings mdgsa_1.12.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/mdgsa.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mdgsa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mdgsa' version '1.12.1'
* 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 whether package 'mdgsa' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
getGOnames: no visible global function definition for
'packageDescription'
getKEGGnames: no visible global function definition for
'packageDescription'
getOntology: no visible global function definition for
'packageDescription'
goLeaves: no visible global function definition for
'packageDescription'
index.normalize: no visible global function definition for 'qqnorm'
index.standardize: no visible global function definition for 'sd'
mdGsa: no visible global function definition for 'quasibinomial'
mdGsa: no visible global function definition for 'glm.fit'
mdGsa: no visible global function definition for 'summary.glm'
mdGsa: no visible global function definition for 'p.adjust'
mdPat: no visible global function definition for 'read.table'
plotMdGsa: no visible global function definition for 'plot'
plotMdGsa: no visible global function definition for 'points'
plotMdGsa: no visible global function definition for 'cov'
plotMdGsa: no visible global function definition for 'qchisq'
plotMdGsa: no visible global function definition for 'lines'
plotMdGsa: no visible global function definition for 'abline'
propagateGO.matrix: no visible global function definition for
'packageDescription'
splitOntologies: no visible global function definition for
'packageDescription'
uvGsa: no visible global function definition for 'quasibinomial'
uvGsa: no visible global function definition for 'glm.fit'
uvGsa: no visible global function definition for 'summary.glm'
uvGsa: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
abline cov glm.fit lines p.adjust packageDescription plot points
qchisq qqnorm quasibinomial read.table sd summary.glm
Consider adding
importFrom("graphics", "abline", "lines", "plot", "points")
importFrom("stats", "cov", "glm.fit", "p.adjust", "qchisq", "qqnorm",
"quasibinomial", "sd", "summary.glm")
importFrom("utils", "packageDescription", "read.table")
to your NAMESPACE file.
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/mdgsa.Rcheck/00check.log'
for details.
mdgsa.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/mdgsa_1.12.1.tar.gz && rm -rf mdgsa.buildbin-libdir && mkdir mdgsa.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mdgsa.buildbin-libdir mdgsa_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL mdgsa_1.12.1.zip && rm mdgsa_1.12.1.tar.gz mdgsa_1.12.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 33262 100 33262 0 0 542k 0 --:--:-- --:--:-- --:--:-- 612k
install for i386
* installing *source* package 'mdgsa' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mdgsa'
finding HTML links ... done
annotFilter html
annotList2mat html
annotMat2list html
getGOnames html
getKEGGnames html
getOntology html
goLeaves html
indexTransform html
mdGsa html
mdPat html
plotMdGsa html
propagateGO html
pval2index html
revList html
splitOntologies html
transferIndex html
uvGsa html
uvPat html
uvSignif html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'mdgsa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mdgsa' as mdgsa_1.12.1.zip
* DONE (mdgsa)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'mdgsa' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
mdgsa.Rcheck/tests_i386/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> BiocGenerics:::testPackage ("mdgsa")
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Filtering annotation by size:
1 small blocks removed.
0 big blocks removed.
3 blocks remain in the annotation.
Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Warning: There are genes in the annotation list which are not
part of the gene universe defined by the ranking index;
they will be eliminated form the annotation.
60% of the genes in the index are annotated in the list.
Filtering annotation by size:
1 small blocks removed.
0 big blocks removed.
3 blocks remain in the annotation.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Using GO.db version: 3.6.0
Using GO.db version: 3.6.0
Loading required package: KEGG.db
Using KEGG.db version: 3.2.3
Using GO.db version: 3.6.0
Analyzed blocks:
time in seconds:
user system elapsed
0.07 0.00 0.07
Using GO.db version: 3.6.0
3miRNAs with annotated targets
2miRNAs without targets
0miRNAs with targets but not in the ranking index
Analyzed blocks:
time in seconds:
user system elapsed
0.02 0.00 0.02
Analyzed blocks:
time in seconds:
user system elapsed
0.02 0.00 0.02
RUNIT TEST PROTOCOL -- Wed Oct 17 03:09:54 2018
***********************************************
Number of test functions: 18
Number of errors: 0
Number of failures: 0
1 Test Suite :
mdgsa RUnit Tests - 18 test functions, 0 errors, 0 failures
Number of test functions: 18
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.06 0.50 11.76
|
mdgsa.Rcheck/tests_x64/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> BiocGenerics:::testPackage ("mdgsa")
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Filtering annotation by size:
1 small blocks removed.
0 big blocks removed.
3 blocks remain in the annotation.
Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Warning: There are genes in the annotation list which are not
part of the gene universe defined by the ranking index;
they will be eliminated form the annotation.
60% of the genes in the index are annotated in the list.
Filtering annotation by size:
1 small blocks removed.
0 big blocks removed.
3 blocks remain in the annotation.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Using GO.db version: 3.6.0
Using GO.db version: 3.6.0
Loading required package: KEGG.db
Using KEGG.db version: 3.2.3
Using GO.db version: 3.6.0
Analyzed blocks:
time in seconds:
user system elapsed
0.01 0.01 0.03
Using GO.db version: 3.6.0
3miRNAs with annotated targets
2miRNAs without targets
0miRNAs with targets but not in the ranking index
Analyzed blocks:
time in seconds:
user system elapsed
0.01 0.00 0.02
Analyzed blocks:
time in seconds:
user system elapsed
0.05 0.00 0.05
RUNIT TEST PROTOCOL -- Wed Oct 17 03:10:06 2018
***********************************************
Number of test functions: 18
Number of errors: 0
Number of failures: 0
1 Test Suite :
mdgsa RUnit Tests - 18 test functions, 0 errors, 0 failures
Number of test functions: 18
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.51 0.31 11.82
|
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mdgsa.Rcheck/examples_i386/mdgsa-Ex.timings
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mdgsa.Rcheck/examples_x64/mdgsa-Ex.timings
|