Yuanyuan Xiao
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/DEDS |
| Branch: RELEASE_3_9 |
| Last Commit: 9f919d0 |
| Last Changed Date: 2019-05-02 11:53:03 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:19:39 -0400 (Wed, 16 Oct 2019).
| Package 403/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEDS 1.58.0 Yuanyuan Xiao
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DEDS |
| Version: 1.58.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEDS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DEDS_1.58.0.tar.gz |
| StartedAt: 2019-10-16 03:06:11 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:07:04 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 52.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEDS.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEDS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DEDS_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DEDS.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'DEDS/DESCRIPTION' ... OK * this is package 'DEDS' 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 'DEDS' can be installed ... OK * 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 ... OK * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: hist.DEDS pairs.DEDS qqnorm.DEDS 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 deds.stat.linkC: warning in matrix(res$t, byrow = FALSE, nc = newX$nT): partial argument match of 'nc' to 'ncol' sam.multiclass.func: warning in matrix(nr = nrow(X), nc = B): partial argument match of 'nr' to 'nrow' sam.multiclass.func: warning in matrix(nr = nrow(X), nc = B): partial argument match of 'nc' to 'ncol' sam.oneclass.func: warning in matrix(nr = nrow(X), nc = B): partial argument match of 'nr' to 'nrow' sam.oneclass.func: warning in matrix(nr = nrow(X), nc = B): partial argument match of 'nc' to 'ncol' sam.twoclass.func: warning in matrix(nr = nrow(X), nc = B): partial argument match of 'nr' to 'nrow' sam.twoclass.func: warning in matrix(nr = nrow(X), nc = B): partial argument match of 'nc' to 'ncol' * checking Rd files ... NOTE prepare_Rd: comp.fdr.Rd:52-54: Dropping empty section \details prepare_Rd: deds.pval.Rd:65-68: Dropping empty section \examples prepare_Rd: hist.DEDS.Rd:47-50: 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 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-3.9-bioc/R/library/DEDS/libs/i386/DEDS.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/DEDS/libs/x64/DEDS.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: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DEDS.Rcheck/00check.log' for details.
DEDS.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DEDS_1.58.0.tar.gz && rm -rf DEDS.buildbin-libdir && mkdir DEDS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEDS.buildbin-libdir DEDS_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DEDS_1.58.0.zip && rm DEDS_1.58.0.tar.gz DEDS_1.58.0.zip
###
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100 3077k 100 3077k 0 0 669k 0 0:00:04 0:00:04 --:--:-- 671k
install for i386
* installing *source* package 'DEDS' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c deds.c -o deds.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c distance.c -o distance.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c input.c -o input.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c manip.c -o manip.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c random.c -o random.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sampling.c -o sampling.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c stat_fun.c -o stat_fun.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o DEDS.dll tmp.def deds.o distance.o input.o manip.o random.o sampling.o stat_fun.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/DEDS.buildbin-libdir/00LOCK-DEDS/00new/DEDS/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DEDS'
finding HTML links ... done
ApoA1 html
DEDS-internal html
affySpikeIn html
aggregateFun html
comp.B html
comp.F html
comp.FC html
comp.SAM html
comp.adjp html
comp.ebayes html
comp.fdr html
comp.modF html
comp.modt html
comp.stat html
comp.t html
comp.unadjp html
deds.chooseTest html
deds.class html
deds.genExtra html
deds.pval html
deds.stat html
deds.stat.linkC html
hist.DEDS html
pairs.DEDS html
qqnorm.DEDS html
topgenes 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 'DEDS' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c deds.c -o deds.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c distance.c -o distance.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c input.c -o input.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c manip.c -o manip.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c random.c -o random.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sampling.c -o sampling.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c stat_fun.c -o stat_fun.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o DEDS.dll tmp.def deds.o distance.o input.o manip.o random.o sampling.o stat_fun.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/DEDS.buildbin-libdir/DEDS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEDS' as DEDS_1.58.0.zip
* DONE (DEDS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DEDS' successfully unpacked and MD5 sums checked
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DEDS.Rcheck/examples_i386/DEDS-Ex.timings
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DEDS.Rcheck/examples_x64/DEDS-Ex.timings
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