Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:19:04 -0400 (Wed, 16 Oct 2019).
Package 1528/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
simpleaffy 2.60.0 Crispin Miller
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: simpleaffy |
Version: 2.60.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:simpleaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings simpleaffy_2.60.0.tar.gz |
StartedAt: 2019-10-16 07:10:12 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 07:13:18 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 185.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: simpleaffy.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:simpleaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings simpleaffy_2.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/simpleaffy.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 'simpleaffy/DESCRIPTION' ... OK * this is package 'simpleaffy' version '2.60.0' * 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 'simpleaffy' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'methods' 'utils' 'grDevices' 'graphics' 'stats' 'BiocGenerics' 'Biobase' 'affy' 'genefilter' 'gcrma' 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 * 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 ... WARNING all: function(..., na.rm) all.present: function(x, calls, no) all: function(..., na.rm) all.present.in.group: function(x, group, members, calls, no) See section 'Generic functions and methods' in the 'Writing R Extensions' manual. Found the following apparent S3 methods exported but not registered: all.present all.present.in.group plot.pairwise.comparison plot.qc.stats 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 hmap.eset :: no visible global function definition for 'var' hmap.pc : : no visible global function definition for 'var' qc.affy: no visible binding for global variable 'var' standard.pearson: no visible global function definition for 'cor' Undefined global functions or variables: cor var Consider adding importFrom("stats", "cor", "var") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'PairComp,ANY,ANY,ANY' generic '[<-' and siglist 'PairComp,ANY,ANY,ANY' All user-level objects in a package (including S4 classes and methods) 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 ... 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/simpleaffy/libs/i386/simpleaffy.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/simpleaffy/libs/x64/simpleaffy.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: 2 WARNINGs, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/simpleaffy.Rcheck/00check.log' for details.
simpleaffy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/simpleaffy_2.60.0.tar.gz && rm -rf simpleaffy.buildbin-libdir && mkdir simpleaffy.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=simpleaffy.buildbin-libdir simpleaffy_2.60.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL simpleaffy_2.60.0.zip && rm simpleaffy_2.60.0.tar.gz simpleaffy_2.60.0.zip ### ############################################################################## ############################################################################## % 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 448k 100 448k 0 0 7296k 0 --:--:-- --:--:-- --:--:-- 8157k install for i386 * installing *source* package 'simpleaffy' ... ** 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 simpleaffy.c -o simpleaffy.o simpleaffy.c: In function 'bgmas': simpleaffy.c:440:30: warning: passing argument 1 of 'REprintf' from incompatible pointer type if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]); ^ In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:88:0, from simpleaffy.c:5: C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R_ext/Print.h:43:6: note: expected 'const char *' but argument is of type 'struct FILE *' void REprintf(const char *, ...); ^ C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.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/simpleaffy.buildbin-libdir/00LOCK-simpleaffy/00new/simpleaffy/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'simpleaffy' finding HTML links ... done PairComp-class html QCStats-class html all.present html all.present.in.group html bg.correct.sa html call.exprs html detection.p.val html get.annotation html get.array.indices html get.array.subset html get.array.subset.affy html get.fold.change.and.t.test html hmap.colors html hmap.eset html hmap.pc html journalpng html justMAS html pairwise.comparison html pairwise.filter html plot.pairwise.comparison html plot.qc.stats html qc html qc.affy html qc.get.alpha1 html qc.get.array html qc.get.probes html qc.get.ratios html qc.get.spikes html qc.have.params html qc.ok html qc.read.file html qc.stats html read.affy html read.affy.mixed html setQCEnvironment html simpleaffy-deprecated html standard.pearson html trad.scatter.plot 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 'simpleaffy' ... ** 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 simpleaffy.c -o simpleaffy.o simpleaffy.c: In function 'bgmas': simpleaffy.c:440:30: warning: passing argument 1 of 'REprintf' from incompatible pointer type if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]); ^ In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:88:0, from simpleaffy.c:5: C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R_ext/Print.h:43:6: note: expected 'const char *' but argument is of type 'struct FILE *' void REprintf(const char *, ...); ^ C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.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/simpleaffy.buildbin-libdir/simpleaffy/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'simpleaffy' as simpleaffy_2.60.0.zip * DONE (simpleaffy) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'simpleaffy' successfully unpacked and MD5 sums checked
simpleaffy.Rcheck/examples_i386/simpleaffy-Ex.timings
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simpleaffy.Rcheck/examples_x64/simpleaffy-Ex.timings
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