Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:23:50 -0400 (Tue, 09 Apr 2019).
Package 1197/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
plier 1.53.0 Crispin Miller
| 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 | WARNINGS | OK | ![]() | ||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: plier |
Version: 1.53.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:plier.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings plier_1.53.0.tar.gz |
StartedAt: 2019-04-09 02:44:19 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 02:44:47 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 28.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: plier.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:plier.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings plier_1.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/plier.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘plier/DESCRIPTION’ ... OK * this is package ‘plier’ version ‘1.53.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘plier’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 ... OK * 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 ... NOTE prepare_Rd: justPlier.Rd:50-52: 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.9-bioc/R/library/plier/libs/plier.so’: Found ‘exit’, possibly from ‘exit’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) 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 examples ... NONE * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/plier.Rcheck/00check.log’ for details.
plier.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL plier ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘plier’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c affyplier.cpp -o affyplier.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c plier_impl.cpp -o plier_impl.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c plieralg.cpp -o plieralg.o plieralg.cpp: In function ‘long int NewtonPlier(plier_data*, double&)’: plieralg.cpp:905:14: warning: variable ‘icount’ set but not used [-Wunused-but-set-variable] long count, icount; ^˜˜˜˜˜ plieralg.cpp: At global scope: plieralg.cpp:49:12: warning: ‘g_ErrorCode’ defined but not used [-Wunused-variable] static int g_ErrorCode=NoError; ^˜˜˜˜˜˜˜˜˜˜ plieralg.cpp: In function ‘long int NewtonPlier(plier_data*, double&)’: plieralg.cpp:1257:24: warning: ‘LogLikelihood’ may be used uninitialized in this function [-Wmaybe-uninitialized] output = LogLikelihood/nSize; ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rwrapper.cpp -o rwrapper.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-plier/00new/plier/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (plier)