Bahman Afsari
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/switchBox |
| Branch: RELEASE_3_11 |
| Last Commit: 7380232 |
| Last Changed Date: 2020-04-27 14:42:47 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:54 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE switchBox PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1769/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| switchBox 1.24.0 Bahman Afsari
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: switchBox |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:switchBox.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings switchBox_1.24.0.tar.gz |
| StartedAt: 2020-10-17 08:45:28 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:46:35 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 66.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: switchBox.Rcheck |
| Warnings: 4 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:switchBox.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings switchBox_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/switchBox.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'switchBox/DESCRIPTION' ... OK
* this is package 'switchBox' version '1.24.0'
* 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 whether package 'switchBox' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpsjCWhG/R.INSTALLc20478c2531/switchBox/man/SWAP.PlotKTSP.TrainTestROC.Rd:35: missing link 'SWAP.GetkTSPTrainTestResults'
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/switchBox.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
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'KTSP.CalculateSignedScore' 'KTSP.tiedRank'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotGenePairBoxplot: no visible global function definition for
'boxplot'
plotGenePairBoxplot: no visible global function definition for
'stripchart'
plotGenePairBoxplot: no visible global function definition for 'legend'
plotGenePairBoxplot: no visible global function definition for 'grid'
plotGenePairClassesBoxplot: no visible global function definition for
'boxplot'
plotGenePairClassesBoxplot: no visible global function definition for
'axis'
plotGenePairClassesBoxplot: no visible global function definition for
'legend'
plotGenePairClassesBoxplot: no visible global function definition for
'abline'
plotGenePairClassesBoxplot: no visible global function definition for
'grid'
plotGenePairScatter: no visible global function definition for 'abline'
plotGenePairScatter: no visible global function definition for 'grid'
plotGenePairScatter: no visible global function definition for 'legend'
plotGenes: no visible global function definition for 'lines'
plotGenes: no visible global function definition for 'grid'
plotGenes: no visible global function definition for 'abline'
plotGenes: no visible global function definition for 'legend'
plotkTSPTrainTestROC: no visible global function definition for 'lines'
plotkTSPTrainTestROC: no visible global function definition for
'legend'
plotkTSPTrainTestROC: no visible global function definition for 'grid'
plotkTSPVotes: no visible global function definition for 'plot.new'
Undefined global functions or variables:
abline axis boxplot grid legend lines plot.new stripchart
Consider adding
importFrom("graphics", "abline", "axis", "boxplot", "grid", "legend",
"lines", "plot.new", "stripchart")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: SWAP.Kby.Measurement.Rd:70-72: Dropping empty section \examples
prepare_Rd: SWAP.Kby.Ttest.Rd:64-66: Dropping empty section \examples
prepare_Rd: SWAP.PlotKTSP.Votes.Rd:54-56: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Package unavailable to check Rd xrefs: 'mammaPrintData'
Missing link or links in documentation object 'SWAP.PlotKTSP.TrainTestROC.Rd':
'SWAP.GetkTSPTrainTestResults'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'SWAP.GetKFoldIndices' 'SWAP.MakeTrainTestData'
'SWAP.ScoreMatrixToVector' 'SWAP.ScoreVectorToMatrix'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'SWAP.Kby.Measurement':
k_opts = list(disjoint = TRUE, measurement = "auc")
Undocumented arguments in documentation object 'SWAP.PlotKTSP.GenePairScatter'
'...'
Undocumented arguments in documentation object 'SWAP.PlotKTSP.Genes'
'colors' 'legends' '...'
Undocumented arguments in documentation object 'SWAP.PlotKTSP.TrainTestROC'
'...'
Undocumented arguments in documentation object 'SWAP.PlotKTSP.Votes'
'...'
Bad \usage lines found in documentation object 'SWAP.Kby.Measurement':
SWAP.Kby.Measurement(inputMat, phenoGroup,
scoreTable, classes, krange,
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/switchBox/libs/i386/switchBox.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/switchBox/libs/x64/switchBox.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SWAP.KTSP.LOO 5.32 0 5.31
* 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: 4 WARNINGs, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/switchBox.Rcheck/00check.log'
for details.
switchBox.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/switchBox_1.24.0.tar.gz && rm -rf switchBox.buildbin-libdir && mkdir switchBox.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=switchBox.buildbin-libdir switchBox_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL switchBox_1.24.0.zip && rm switchBox_1.24.0.tar.gz switchBox_1.24.0.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 461k 100 461k 0 0 3235k 0 --:--:-- --:--:-- --:--:-- 3417k
install for i386
* installing *source* package 'switchBox' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o
CalculateSignedScoreCore.cc: In function 'void CalculateSignedScoreCore(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*, double*, double*, double*)':
CalculateSignedScoreCore.cc:36:26: warning: variable 'pairsNo' set but not used [-Wunused-but-set-variable]
int i,j,l,countplace,pairsNo;
^~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreCoreTieHandler.cc -o CalculateSignedScoreCoreTieHandler.o
CalculateSignedScoreCoreTieHandler.cc: In function 'void CalculateSignedScoreCoreTieHandler(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*)':
CalculateSignedScoreCoreTieHandler.cc:49:12: warning: unused variable 'score1' [-Wunused-variable]
double score1, score2, type;
^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o
CalculateSignedScoreRestrictedPairsCore.cc: In function 'void CalculateSignedScoreRestrictedPairsCore(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*)':
CalculateSignedScoreRestrictedPairsCore.cc:22:11: warning: variable 'countplace' set but not used [-Wunused-but-set-variable]
int i,l,countplace,pairsNo;
^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreRestrictedPairsCoreTieHandler.cc -o CalculateSignedScoreRestrictedPairsCoreTieHandler.o
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc: In function 'void CalculateSignedScoreRestrictedPairsCoreTieHandler(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*)':
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:25:11: warning: unused variable 'countplace' [-Wunused-variable]
int i,l,countplace,pairsNo;
^~~~~~~~~~
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:10: warning: unused variable 'score1' [-Wunused-variable]
double score1, score2, type;
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rinit.c -o rinit.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vect2compC.cc -o vect2compC.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o switchBox.dll tmp.def CalculateSignedScoreCore.o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCoreTieHandler.o rinit.o vect2compC.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/switchBox.buildbin-libdir/00LOCK-switchBox/00new/switchBox/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'switchBox'
finding HTML links ... done
KTSP.Classify html
KTSP.Train html
SWAP.Calculate.BasicTSPScores html
SWAP.Calculate.SignedTSPScores html
SWAP.CalculateScores html
SWAP.CalculateSignedScore html
SWAP.Filter.Wilcoxon html
SWAP.GetKTSP.PredictionStats html
SWAP.GetKTSP.Result html
SWAP.GetKTSP.TrainTestResults html
SWAP.KTSP.CV html
SWAP.KTSP.Classify html
SWAP.KTSP.LOO html
SWAP.KTSP.Statistic html
SWAP.KTSP.Train html
SWAP.Kby.Measurement html
SWAP.Kby.Ttest html
SWAP.MakeTSPTable html
SWAP.PlotKTSP.GenePairBoxplot html
SWAP.PlotKTSP.GenePairClassesBoxplot html
SWAP.PlotKTSP.GenePairScatter html
SWAP.PlotKTSP.Genes html
SWAP.PlotKTSP.TrainTestROC html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpsjCWhG/R.INSTALLc20478c2531/switchBox/man/SWAP.PlotKTSP.TrainTestROC.Rd:35: missing link 'SWAP.GetkTSPTrainTestResults'
SWAP.PlotKTSP.Votes html
SWAP.Train.1TSP html
SWAP.Train.KTSP html
matTesting html
matTraining html
switchBox-package html
testingGroup html
trainingGroup html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'switchBox' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o
CalculateSignedScoreCore.cc: In function 'void CalculateSignedScoreCore(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*, double*, double*, double*)':
CalculateSignedScoreCore.cc:36:26: warning: variable 'pairsNo' set but not used [-Wunused-but-set-variable]
int i,j,l,countplace,pairsNo;
^~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreCoreTieHandler.cc -o CalculateSignedScoreCoreTieHandler.o
CalculateSignedScoreCoreTieHandler.cc: In function 'void CalculateSignedScoreCoreTieHandler(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*)':
CalculateSignedScoreCoreTieHandler.cc:49:12: warning: unused variable 'score1' [-Wunused-variable]
double score1, score2, type;
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o
CalculateSignedScoreRestrictedPairsCore.cc: In function 'void CalculateSignedScoreRestrictedPairsCore(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*)':
CalculateSignedScoreRestrictedPairsCore.cc:22:11: warning: variable 'countplace' set but not used [-Wunused-but-set-variable]
int i,l,countplace,pairsNo;
^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateSignedScoreRestrictedPairsCoreTieHandler.cc -o CalculateSignedScoreRestrictedPairsCoreTieHandler.o
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc: In function 'void CalculateSignedScoreRestrictedPairsCoreTieHandler(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*)':
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:25:11: warning: unused variable 'countplace' [-Wunused-variable]
int i,l,countplace,pairsNo;
^~~~~~~~~~
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:10: warning: unused variable 'score1' [-Wunused-variable]
double score1, score2, type;
^~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rinit.c -o rinit.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vect2compC.cc -o vect2compC.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o switchBox.dll tmp.def CalculateSignedScoreCore.o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCoreTieHandler.o rinit.o vect2compC.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/switchBox.buildbin-libdir/switchBox/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'switchBox' as switchBox_1.24.0.zip
* DONE (switchBox)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'switchBox' successfully unpacked and MD5 sums checked
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switchBox.Rcheck/examples_i386/switchBox-Ex.timings
|
switchBox.Rcheck/examples_x64/switchBox-Ex.timings
|