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This page was generated on 2022-04-13 12:06:45 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

INSTALL results for IRISFGM on tokay2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 955/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRISFGM 1.2.0  (landing page)
Yuzhou Chang
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/IRISFGM
git_branch: RELEASE_3_14
git_last_commit: d9e123f
git_last_commit_date: 2021-10-26 13:07:08 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: IRISFGM
Version: 1.2.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/IRISFGM_1.2.0.tar.gz && rm -rf IRISFGM.buildbin-libdir && mkdir IRISFGM.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRISFGM.buildbin-libdir IRISFGM_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL IRISFGM_1.2.0.zip && rm IRISFGM_1.2.0.tar.gz IRISFGM_1.2.0.zip
StartedAt: 2022-04-12 07:26:14 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:29:59 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 224.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/IRISFGM_1.2.0.tar.gz && rm -rf IRISFGM.buildbin-libdir && mkdir IRISFGM.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRISFGM.buildbin-libdir IRISFGM_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL IRISFGM_1.2.0.zip && rm IRISFGM_1.2.0.tar.gz IRISFGM_1.2.0.zip
###
##############################################################################
##############################################################################


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100  863k  100  863k    0     0   699k      0  0:00:01  0:00:01 --:--:--  699k

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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/IRISFGM.buildbin-libdir/IRISFGM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRISFGM' as IRISFGM_1.2.0.zip
* DONE (IRISFGM)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'IRISFGM' successfully unpacked and MD5 sums checked