BioC 3.4: INSTALL report for scran on tokay1

Package: scran

Version: 1.2.2

Command: rm -rf scran.buildbin-libdir && mkdir scran.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.4/bioc/src/contrib/scran_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=scran.buildbin-libdir --merge-multiarch scran_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL scran_1.2.2.zip && rm scran_1.2.2.tar.gz scran_1.2.2.zip

StartedAt: 2017-04-14 18:16:38 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 18:17:12 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 34.7 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   rm -rf scran.buildbin-libdir && mkdir scran.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.4/bioc/src/contrib/scran_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=scran.buildbin-libdir --merge-multiarch scran_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL scran_1.2.2.zip  && rm scran_1.2.2.tar.gz scran_1.2.2.zip
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install for i386

* installing *source* package 'scran' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c compute_CV2.cpp -o compute_CV2.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c compute_cordist.cpp -o compute_cordist.o
compute_cordist.cpp: In instantiation of 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]':
compute_cordist.cpp:145:59:   required from here
compute_cordist.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t s=0; s<slen; ++s) {
                       ^
compute_cordist.cpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s]<0 || sptr[s]>=MAT.nrow) {
                                 ^
compute_cordist.cpp:85:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t s=0; s<slen; ++s) {
                               ^
compute_cordist.cpp:92:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t s=0; s<slen; ++s) {
                               ^
compute_cordist.cpp:117:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (size_t s=0; s<slen; ++s) {
                                   ^
compute_cordist.cpp: In instantiation of 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]':
compute_cordist.cpp:147:62:   required from here
compute_cordist.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t s=0; s<slen; ++s) {
                       ^
compute_cordist.cpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s]<0 || sptr[s]>=MAT.nrow) {
                                 ^
compute_cordist.cpp:85:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t s=0; s<slen; ++s) {
                               ^
compute_cordist.cpp:92:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t s=0; s<slen; ++s) {
                               ^
compute_cordist.cpp:117:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (size_t s=0; s<slen; ++s) {
                                   ^
compute_cordist.cpp: In instantiation of 'double** average_ranks(const T*, const matrix_info&, const int*, int) [with T = int]':
compute_cordist.cpp:78:59:   required from 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]'
compute_cordist.cpp:145:59:   required from here
compute_cordist.cpp:15:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t s=0; s<subset_len; ++s) {
                           ^
compute_cordist.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t s=0; s<subset_len; ++s) {
                           ^
compute_cordist.cpp:30:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (s==subset_len-1 || collected[s].first!=collected[s+1].first) {
                  ^
compute_cordist.cpp: In instantiation of 'double** average_ranks(const T*, const matrix_info&, const int*, int) [with T = double]':
compute_cordist.cpp:78:59:   required from 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]'
compute_cordist.cpp:147:62:   required from here
compute_cordist.cpp:15:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t s=0; s<subset_len; ++s) {
                           ^
compute_cordist.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t s=0; s<subset_len; ++s) {
                           ^
compute_cordist.cpp:30:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (s==subset_len-1 || collected[s].first!=collected[s+1].first) {
                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c compute_rho.cpp -o compute_rho.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c estimate_variance.cpp -o estimate_variance.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c forge_system.cpp -o forge_system.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c matrix_info.cpp -o matrix_info.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c run_dormqr.cpp -o run_dormqr.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c shuffle_scores.cpp -o shuffle_scores.o
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(SEXP, const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]':
shuffle_scores.cpp:104:120:   required from here
shuffle_scores.cpp:24:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (start < 0 || last > emat.ncol) { throw std::runtime_error("cell indices are out of range"); }
                           ^
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(SEXP, const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]':
shuffle_scores.cpp:106:123:   required from here
shuffle_scores.cpp:24:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def compute_CV2.o compute_cordist.o compute_rho.o estimate_variance.o forge_system.o init.o matrix_info.o run_dormqr.o shuffle_scores.o -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/scran.buildbin-libdir/scran/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'scran' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c compute_CV2.cpp -o compute_CV2.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c compute_cordist.cpp -o compute_cordist.o
compute_cordist.cpp: In instantiation of 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]':
compute_cordist.cpp:145:59:   required from here
compute_cordist.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t s=0; s<slen; ++s) {
                       ^
compute_cordist.cpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s]<0 || sptr[s]>=MAT.nrow) {
                                 ^
compute_cordist.cpp:85:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t s=0; s<slen; ++s) {
                               ^
compute_cordist.cpp:92:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t s=0; s<slen; ++s) {
                               ^
compute_cordist.cpp:117:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (size_t s=0; s<slen; ++s) {
                                   ^
compute_cordist.cpp: In instantiation of 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]':
compute_cordist.cpp:147:62:   required from here
compute_cordist.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t s=0; s<slen; ++s) {
                       ^
compute_cordist.cpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s]<0 || sptr[s]>=MAT.nrow) {
                                 ^
compute_cordist.cpp:85:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t s=0; s<slen; ++s) {
                               ^
compute_cordist.cpp:92:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t s=0; s<slen; ++s) {
                               ^
compute_cordist.cpp:117:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (size_t s=0; s<slen; ++s) {
                                   ^
compute_cordist.cpp: In instantiation of 'double** average_ranks(const T*, const matrix_info&, const int*, int) [with T = int]':
compute_cordist.cpp:78:59:   required from 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]'
compute_cordist.cpp:145:59:   required from here
compute_cordist.cpp:15:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t s=0; s<subset_len; ++s) {
                           ^
compute_cordist.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t s=0; s<subset_len; ++s) {
                           ^
compute_cordist.cpp:30:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (s==subset_len-1 || collected[s].first!=collected[s+1].first) {
                  ^
compute_cordist.cpp: In instantiation of 'double** average_ranks(const T*, const matrix_info&, const int*, int) [with T = double]':
compute_cordist.cpp:78:59:   required from 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]'
compute_cordist.cpp:147:62:   required from here
compute_cordist.cpp:15:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t s=0; s<subset_len; ++s) {
                           ^
compute_cordist.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t s=0; s<subset_len; ++s) {
                           ^
compute_cordist.cpp:30:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (s==subset_len-1 || collected[s].first!=collected[s+1].first) {
                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c compute_rho.cpp -o compute_rho.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c estimate_variance.cpp -o estimate_variance.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c forge_system.cpp -o forge_system.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c matrix_info.cpp -o matrix_info.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c run_dormqr.cpp -o run_dormqr.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c shuffle_scores.cpp -o shuffle_scores.o
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(SEXP, const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]':
shuffle_scores.cpp:104:120:   required from here
shuffle_scores.cpp:24:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (start < 0 || last > emat.ncol) { throw std::runtime_error("cell indices are out of range"); }
                           ^
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(SEXP, const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]':
shuffle_scores.cpp:106:123:   required from here
shuffle_scores.cpp:24:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def compute_CV2.o compute_cordist.o compute_rho.o estimate_variance.o forge_system.o init.o matrix_info.o run_dormqr.o shuffle_scores.o -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/scran.buildbin-libdir/scran/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scran' as scran_1.2.2.zip
* DONE (scran)
* installing to library 'C:/Users/biocbuild/bbs-3.4-bioc/R/library'
package 'scran' successfully unpacked and MD5 sums checked