Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:43 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the iClusterPlus package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iClusterPlus.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 907/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iClusterPlus 1.30.0 (landing page) Qianxing Mo
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: iClusterPlus |
Version: 1.30.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iClusterPlus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iClusterPlus_1.30.0.tar.gz |
StartedAt: 2022-04-12 21:18:27 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 21:23:00 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 273.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: iClusterPlus.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iClusterPlus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iClusterPlus_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/iClusterPlus.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'iClusterPlus/DESCRIPTION' ... OK * this is package 'iClusterPlus' version '1.30.0' * 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 'iClusterPlus' can be installed ... OK * checking installed package size ... NOTE installed size is 23.6Mb sub-directories of 1Mb or more: data 17.9Mb doc 4.2Mb libs 1.1Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Found a 'configure.in' file: 'configure.ac' has long been preferred. * 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CNregions: no visible binding for global variable 'chromosome' CNregions: no visible binding for global variable 'num.mark' CNregions: no visible global function definition for 'GRanges' CNregions: no visible global function definition for 'IRanges' CNregions: no visible global function definition for 'findOverlaps' CNregions : get.medoid: no visible global function definition for 'pam' classError: no visible global function definition for 'mapClass' plotHMBayes: no visible global function definition for 'bluered' plotHMBayes : my.panel.levelplot: no visible global function definition for 'panel.levelplot' plotHMBayes : my.panel.levelplot: no visible global function definition for 'panel.abline' plotHMBayes : my.panel.levelplot.2: no visible global function definition for 'panel.levelplot' plotHMBayes : my.panel.levelplot.2: no visible global function definition for 'panel.abline' plotHMBayes: no visible global function definition for 'levelplot' plotHeatmap: no visible global function definition for 'bluered' plotHeatmap : my.panel.levelplot: no visible global function definition for 'panel.levelplot' plotHeatmap : my.panel.levelplot: no visible global function definition for 'panel.abline' plotHeatmap : my.panel.levelplot.2: no visible global function definition for 'panel.levelplot' plotHeatmap : my.panel.levelplot.2: no visible global function definition for 'panel.abline' plotHeatmap: no visible global function definition for 'levelplot' tune.iCluster2: no visible binding for global variable 'glp' tune.iClusterPlus: no visible binding for global variable 'glp' Undefined global functions or variables: GRanges IRanges bluered chromosome findOverlaps glp levelplot mapClass num.mark pam panel.abline panel.levelplot * 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 LazyData ... WARNING LazyData DB of 17.8 MB without LazyDataCompression set See ยง1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... 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-3.14-bioc/R/library/iClusterPlus/libs/i386/iClusterPlus.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Found 'rand', possibly from 'rand' (C) File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/iClusterPlus/libs/x64/iClusterPlus.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'rand', possibly from 'rand' (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 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 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.R' 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-3.14-bioc/meat/iClusterPlus.Rcheck/00check.log' for details.
iClusterPlus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/iClusterPlus_1.30.0.tar.gz && rm -rf iClusterPlus.buildbin-libdir && mkdir iClusterPlus.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iClusterPlus.buildbin-libdir iClusterPlus_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL iClusterPlus_1.30.0.zip && rm iClusterPlus_1.30.0.tar.gz iClusterPlus_1.30.0.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 0 20.2M 0 22757 0 0 192k 0 0:01:47 --:--:-- 0:01:47 191k 5 20.2M 5 1223k 0 0 1093k 0 0:00:18 0:00:01 0:00:17 1093k 16 20.2M 16 3347k 0 0 1580k 0 0:00:13 0:00:02 0:00:11 1580k 30 20.2M 30 6413k 0 0 2056k 0 0:00:10 0:00:03 0:00:07 2056k 50 20.2M 50 10.1M 0 0 2524k 0 0:00:08 0:00:04 0:00:04 2524k 72 20.2M 72 14.6M 0 0 2946k 0 0:00:07 0:00:05 0:00:02 3010k 100 20.2M 100 20.2M 0 0 3393k 0 0:00:06 0:00:06 --:--:-- 3909k install for i386 * installing *source* package 'iClusterPlus' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c iClusterBayes.c -o iClusterBayes.o iClusterBayes.c: In function 'mcmcBayes': iClusterBayes.c:1212:28: warning: variable 'Zdraw' set but not used [-Wunused-but-set-variable] int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k; ^~~~~ iClusterBayes.c:1212:20: warning: variable 'Zburnin' set but not used [-Wunused-but-set-variable] int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k; ^~~~~~~ iClusterBayes.c:1600:13: warning: 'gb4' may be used uninitialized in this function [-Wmaybe-uninitialized] gb4[ID] = b4[ID]*gamma4[j]; ~~~~~~~~^~~~~~~~~~~~~~~~~~ iClusterBayes.c:1575:13: warning: 'gb3' may be used uninitialized in this function [-Wmaybe-uninitialized] gb3[ID] = b3[ID]*gamma3[j]; ~~~~~~~~^~~~~~~~~~~~~~~~~~ iClusterBayes.c:1475:5: warning: 'gb2' may be used uninitialized in this function [-Wmaybe-uninitialized] mcmcMix6d(meanZ,lastZ,nkZbd,sdev, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty0,&p0,a0,gb0,con0,cat0,sigma0, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty1,&p1,a1,gb1,con1,cat1,sigma1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty2,&p2,a2,gb2,con2,cat2,sigma2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty3,&p3,a3,gb3,con3,cat3,sigma3, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty4,&p4,a4,gb4,con4,cat4,sigma4, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iClusterBayes.c:1475:5: warning: 'gb1' may be used uninitialized in this function [-Wmaybe-uninitialized] iClusterBayes.c:1475:5: warning: 'gb0' may be used uninitialized in this function [-Wmaybe-uninitialized] iClusterBayes.c:1625:13: warning: 'gb5' may be used uninitialized in this function [-Wmaybe-uninitialized] gb5[ID] = b5[ID]*gamma5[j]; ~~~~~~~~^~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c iClusterPlus.c -o iClusterPlus.o "C:/rtools40/mingw32/bin/"gfortran -fno-optimize-sibling-calls -fdefault-real-8 -ffixed-form -O2 -mfpmath=sse -msse2 -mstackrealign -c newGLMnet.f90 -o newGLMnet.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o iClusterPlus.dll tmp.def iClusterBayes.o iClusterPlus.o newGLMnet.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/iClusterPlus.buildbin-libdir/00LOCK-iClusterPlus/00new/iClusterPlus/libs/i386 ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'iClusterPlus' finding HTML links ... done CNregions html breast.chr17 html compute.pod html coord html gbm html glp html iCluster html iCluster2 html iClusterBayes html iClusterPlus html plotHMBayes html plotHeatmap html plotRI html plotiCluster html simuResult html tune.iCluster2 html tune.iClusterBayes html tune.iClusterPlus html utility html variation.hg18.v10.nov.2010 html ** building package indices ** installing vignettes 'iClusterPlus.Rnw' using 'UTF-8' ** 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 'iClusterPlus' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c iClusterBayes.c -o iClusterBayes.o iClusterBayes.c: In function 'mcmcBayes': iClusterBayes.c:1212:28: warning: variable 'Zdraw' set but not used [-Wunused-but-set-variable] int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k; ^~~~~ iClusterBayes.c:1212:20: warning: variable 'Zburnin' set but not used [-Wunused-but-set-variable] int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k; ^~~~~~~ iClusterBayes.c:1446:13: warning: 'gb4' may be used uninitialized in this function [-Wmaybe-uninitialized] gb4[ID] = b4[ID]*gamma4[j]; ~~~~~~~~^~~~~~~~~~~~~~~~~~ iClusterBayes.c:1431:13: warning: 'gb3' may be used uninitialized in this function [-Wmaybe-uninitialized] gb3[ID] = b3[ID]*gamma3[j]; ~~~~~~~~^~~~~~~~~~~~~~~~~~ iClusterBayes.c:1475:5: warning: 'gb2' may be used uninitialized in this function [-Wmaybe-uninitialized] mcmcMix6d(meanZ,lastZ,nkZbd,sdev, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty0,&p0,a0,gb0,con0,cat0,sigma0, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty1,&p1,a1,gb1,con1,cat1,sigma1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty2,&p2,a2,gb2,con2,cat2,sigma2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty3,&p3,a3,gb3,con3,cat3,sigma3, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty4,&p4,a4,gb4,con4,cat4,sigma4, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iClusterBayes.c:1475:5: warning: 'gb1' may be used uninitialized in this function [-Wmaybe-uninitialized] iClusterBayes.c:1475:5: warning: 'gb0' may be used uninitialized in this function [-Wmaybe-uninitialized] iClusterBayes.c:1461:13: warning: 'gb5' may be used uninitialized in this function [-Wmaybe-uninitialized] gb5[ID] = b5[ID]*gamma5[j]; ~~~~~~~~^~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c iClusterPlus.c -o iClusterPlus.o "C:/rtools40/mingw64/bin/"gfortran -fno-optimize-sibling-calls -fdefault-real-8 -ffixed-form -O2 -mfpmath=sse -msse2 -mstackrealign -c newGLMnet.f90 -o newGLMnet.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o iClusterPlus.dll tmp.def iClusterBayes.o iClusterPlus.o newGLMnet.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/iClusterPlus.buildbin-libdir/iClusterPlus/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'iClusterPlus' as iClusterPlus_1.30.0.zip * DONE (iClusterPlus) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'iClusterPlus' successfully unpacked and MD5 sums checked
iClusterPlus.Rcheck/tests_i386/runTests.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("iClusterPlus") RUNIT TEST PROTOCOL -- Tue Apr 12 21:21:24 2022 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : iClusterPlus RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 > > > proc.time() user system elapsed 90.51 0.18 92.14 |
iClusterPlus.Rcheck/tests_x64/runTests.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("iClusterPlus") RUNIT TEST PROTOCOL -- Tue Apr 12 21:22:51 2022 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : iClusterPlus RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 > > > proc.time() user system elapsed 80.81 0.21 86.86 |
iClusterPlus.Rcheck/examples_i386/iClusterPlus-Ex.timings
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iClusterPlus.Rcheck/examples_x64/iClusterPlus-Ex.timings
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