Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the IRISFGM package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IRISFGM.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 943/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IRISFGM 1.0.0 (landing page) Yuzhou Chang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: IRISFGM |
Version: 1.0.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IRISFGM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings IRISFGM_1.0.0.tar.gz |
StartedAt: 2021-10-15 00:53:21 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:02:37 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 556.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IRISFGM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IRISFGM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings IRISFGM_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/IRISFGM.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'IRISFGM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'IRISFGM' version '1.0.0' * package encoding: UTF-8 * 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 'IRISFGM' 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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-3.13-bioc/R/library/IRISFGM/libs/i386/IRISFGM.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) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRISFGM/libs/x64/IRISFGM.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) 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed RunDimensionReduction 5.01 0.07 5.08 * 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 NOTE See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/IRISFGM.Rcheck/00check.log' for details.
IRISFGM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/IRISFGM_1.0.0.tar.gz && rm -rf IRISFGM.buildbin-libdir && mkdir IRISFGM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRISFGM.buildbin-libdir IRISFGM_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL IRISFGM_1.0.0.zip && rm IRISFGM_1.0.0.tar.gz IRISFGM_1.0.0.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 5 863k 5 47187 0 0 298k 0 0:00:02 --:--:-- 0:00:02 297k 100 863k 100 863k 0 0 1886k 0 --:--:-- --:--:-- --:--:-- 1886k install for i386 * installing *source* package 'IRISFGM' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cpp -o cluster.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c expand.cpp -o expand.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c get_options.cpp -o get_options.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getline.c -o getline.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main.cpp -o main.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c make_graph.cpp -o make_graph.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_irisfgm.cpp -o rcpp_irisfgm.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_array.cpp -o read_array.o read_array.cpp: In function 'void discretize_new(const char*)': read_array.cpp:883:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] for (std::size_t j = 0; j < cols; j++) { ~~^~~~~~ read_array.cpp: In function 'void discretize_rpkm(const char*)': read_array.cpp:1377:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] for (std::size_t j = 0; j < cols; j++) { ~~^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c struct.cpp -o struct.o struct.cpp: In function 'void uglyTime(const char*, ...)': struct.cpp:75:15: warning: variable 'lastTime' set but not used [-Wunused-but-set-variable] static long lastTime = 0; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_block.cpp -o write_block.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o IRISFGM.dll tmp.def RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.o -fopenmp -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/IRISFGM.buildbin-libdir/00LOCK-IRISFGM/00new/IRISFGM/libs/i386 ** R ** data ** byte-compile and prepare package for lazy loading Creating a generic function from function 'ReadFrom10X_h5' in package 'IRISFGM' Creating a generic function from function 'ReadFrom10X_folder' in package 'IRISFGM' ** help *** installing help indices converting help for package 'IRISFGM' finding HTML links ... done AddMeta html BIC_LTMG html BIC_ZIMG html CLUSTERING html CalBinaryMultiSignal html CalBinarySingleSignal html CreateIRISFGMObject html DimReduce-class html DotPlotPathway html FindClassBasedOnMC html FindGlobalMarkers html finding level-2 HTML links ... done FindMarker html Fit_LTMG html GRAPH html GetBinaryMultiSignal html GetBinarySingleSignal html GetLTMGmatrix html Global_Zcut html IRISFGM-class html InverseMillsRatio html KS_LTMG html KS_ZIMG html LTMG html LogSeparateKRpkmNew html LogSeparateKRpkmNewLR html MCL html MINUS html MIN_return html Pi_Zj_Zcut_new html PlotDimension html PlotHeatmap html PlotMarkerHeatmap html PlotMeta html PlotModuleNetwork html PlotNetwork html ProcessData html Pure_CDF html ReadFrom10X_folder html ReadFrom10X_h5 html RunBicluster html RunClassification html RunDimensionReduction html RunDiscretization html RunLTMG html RunPathway html SC html SeparateKRpkmNew html SeparateKRpkmNew2 html SeparateKRpkmNewLR html SeparateKRpkmNewLRPlus html SeparateKRpkmNewp html State_return html SubsetData html dot-IDConvert html dot-RunGO html dot-RunKEGG html dot-generateNetObject html dot-getBlock html dot-runBiclusterBaseOnDiscretization html dot-runBiclusterBaseOnLTMG html dot-separateBic html example_object html getMeta html qubic 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 'IRISFGM' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cpp -o cluster.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c expand.cpp -o expand.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c get_options.cpp -o get_options.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getline.c -o getline.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main.cpp -o main.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c make_graph.cpp -o make_graph.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_irisfgm.cpp -o rcpp_irisfgm.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_array.cpp -o read_array.o read_array.cpp: In function 'void discretize_new(const char*)': read_array.cpp:882:21: warning: format '%d' expects argument of type 'int', but argument 4 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]); ^~~~~~~ read_array.cpp:883:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] for (std::size_t j = 0; j < cols; j++) { ~~^~~~~~ read_array.cpp: In function 'void discretize_rpkm(const char*)': read_array.cpp:1376:21: warning: format '%d' expects argument of type 'int', but argument 4 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]); ^~~~~~~ read_array.cpp:1377:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] for (std::size_t j = 0; j < cols; j++) { ~~^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c struct.cpp -o struct.o struct.cpp: In function 'void uglyTime(const char*, ...)': struct.cpp:75:15: warning: variable 'lastTime' set but not used [-Wunused-but-set-variable] static long lastTime = 0; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_block.cpp -o write_block.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o IRISFGM.dll tmp.def RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/IRISFGM.buildbin-libdir/IRISFGM/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'IRISFGM' as IRISFGM_1.0.0.zip * DONE (IRISFGM) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'IRISFGM' successfully unpacked and MD5 sums checked
IRISFGM.Rcheck/examples_i386/IRISFGM-Ex.timings
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IRISFGM.Rcheck/examples_x64/IRISFGM-Ex.timings
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