Keith Sheppard
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/maanova |
| Branch: RELEASE_3_11 |
| Last Commit: 13c76ca |
| Last Changed Date: 2020-04-27 14:12:05 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:59 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE maanova PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 967/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| maanova 1.58.0 Keith Sheppard
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: maanova |
| Version: 1.58.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maanova.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings maanova_1.58.0.tar.gz |
| StartedAt: 2020-10-17 05:35:11 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:36:20 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 69.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: maanova.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maanova.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings maanova_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/maanova.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 'maanova/DESCRIPTION' ... OK * this is package 'maanova' version '1.58.0' * 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 'maanova' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcPRnKX/R.INSTALL16545fbe5c4c/maanova/man/geneprofile.Rd:31: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/maanova.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 'library' or 'require' calls in package code: 'qvalue' 'snow' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: plot.consensus.hc plot.consensus.kmean print.madata print.summary.madata print.summary.mamodel subset.madata summary.madata summary.mamodel transform.madata transform.rawdata See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE fdr: no visible global function definition for 'qvalue' matest: no visible global function definition for 'makeMPIcluster' matest: no visible global function definition for 'clusterApply' matest: no visible global function definition for 'clusterEvalQ' matest: no visible global function definition for 'stopCluster' Undefined global functions or variables: clusterApply clusterEvalQ makeMPIcluster qvalue stopCluster * 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 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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/maanova/libs/i386/maanova.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/maanova/libs/x64/maanova.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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/maanova.Rcheck/00check.log' for details.
maanova.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/maanova_1.58.0.tar.gz && rm -rf maanova.buildbin-libdir && mkdir maanova.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maanova.buildbin-libdir maanova_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL maanova_1.58.0.zip && rm maanova_1.58.0.tar.gz maanova_1.58.0.zip
###
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install for i386
* installing *source* package 'maanova' ...
** using staged installation
** libs
"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 makeratio.c -o makeratio.o
"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 masvd.c -o masvd.o
masvd.c:114:2: warning: "/*" within comment [-Wcomment]
/* work on a copy of x */
masvd.c:154:1: warning: "/*" within comment [-Wcomment]
/*#ifndef IEEE_754
masvd.c:161:5: warning: "/*" within comment [-Wcomment]
/* work on a copy of x */
masvd.c:165:2: warning: "/*" within comment [-Wcomment]
/* ask for optimal size of work array */
masvd.c:189:2: warning: "/*" within comment [-Wcomment]
/* ask for optimal size of work array */
"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 shift.c -o shift.o
shift.c: In function 'shift':
shift.c:27:13: warning: unused variable 'k' [-Wunused-variable]
int i, j, k;
^
"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 util.c -o util.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o maanova.dll tmp.def makeratio.o masvd.o shift.o util.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -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/maanova.buildbin-libdir/00LOCK-maanova/00new/maanova/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'maanova'
finding HTML links ... done
PairContrast html
Rmaanova.version html
abf1 html
adjPval html
arrayview html
consensus html
dyeswapfilter html
fill.missing html
fitmaanova html
fom html
geneprofile html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcPRnKX/R.INSTALL16545fbe5c4c/maanova/man/geneprofile.Rd:31: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
gridcheck html
kidney html
maanova-internal html
macluster html
matest html
read.madata html
resiplot html
riplot html
subset.madata html
summarytable html
transform.madata html
varplot html
volcano html
write.madata 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 'maanova' ...
** libs
"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 makeratio.c -o makeratio.o
"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 masvd.c -o masvd.o
masvd.c:114:2: warning: "/*" within comment [-Wcomment]
/* work on a copy of x */
masvd.c:154:1: warning: "/*" within comment [-Wcomment]
/*#ifndef IEEE_754
masvd.c:161:5: warning: "/*" within comment [-Wcomment]
/* work on a copy of x */
masvd.c:165:2: warning: "/*" within comment [-Wcomment]
/* ask for optimal size of work array */
masvd.c:189:2: warning: "/*" within comment [-Wcomment]
/* ask for optimal size of work array */
"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 shift.c -o shift.o
shift.c: In function 'shift':
shift.c:27:13: warning: unused variable 'k' [-Wunused-variable]
int i, j, k;
^
"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 util.c -o util.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o maanova.dll tmp.def makeratio.o masvd.o shift.o util.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -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/maanova.buildbin-libdir/maanova/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maanova' as maanova_1.58.0.zip
* DONE (maanova)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'maanova' successfully unpacked and MD5 sums checked
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maanova.Rcheck/examples_i386/maanova-Ex.timings
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maanova.Rcheck/examples_x64/maanova-Ex.timings
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