scran 1.4.5
Aaron Lun
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/scran | | Last Changed Rev: 131271 / Revision: 131943 | | Last Changed Date: 2017-07-17 04:49:26 -0400 (Mon, 17 Jul 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | 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://172.29.0.4/BBS/3.5/bioc/src/contrib/scran_1.4.5.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=scran.buildbin-libdir --merge-multiarch scran_1.4.5.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL scran_1.4.5.zip && rm scran_1.4.5.tar.gz scran_1.4.5.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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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˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c build_snn.cpp -o build_snn.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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˜1.5-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, SEXP) [with T = int; SEXP = SEXPREC*]':
compute_cordist.cpp:142:73: required from here
compute_cordist.cpp:119:35: 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, SEXP) [with T = double; SEXP = SEXPREC*]':
compute_cordist.cpp:144:76: required from here
compute_cordist.cpp:119:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
compute_cordist.cpp: In instantiation of 'void average_ranks(const T*, const matrix_info&, const int*, int, double*) [with T = int]':
compute_cordist.cpp:79:58: required from 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]'
compute_cordist.cpp:142:73: required from here
compute_cordist.cpp:12:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:25:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:29:18: 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:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp: In instantiation of 'void average_ranks(const T*, const matrix_info&, const int*, int, double*) [with T = double]':
compute_cordist.cpp:79:58: required from 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]'
compute_cordist.cpp:144:76: required from here
compute_cordist.cpp:12:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:25:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:29:18: 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:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c compute_rho.cpp -o compute_rho.o
compute_rho.cpp: In function 'SEXPREC* combine_corP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
compute_rho.cpp:421:31: warning: unused variable 'temp_abs_rho' [-Wunused-variable]
double temp_combined, temp_abs_rho;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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˜1.5-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˜1.5-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˜1.5-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˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c overlap_exprs.cpp -o overlap_exprs.o
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, T) [with T = int; SEXP = SEXPREC*]':
overlap_exprs.cpp:138:96: required from here
overlap_exprs.cpp:26:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (cursource[j]<1 || cursource[j]>ncells) {
^
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, T) [with T = double; SEXP = SEXPREC*]':
overlap_exprs.cpp:140:96: required from here
overlap_exprs.cpp:26:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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˜1.5-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 build_snn.o compute_CV2.o compute_cordist.o compute_rho.o estimate_variance.o forge_system.o init.o matrix_info.o overlap_exprs.o run_dormqr.o shuffle_scores.o -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c build_snn.cpp -o build_snn.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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˜1.5-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, SEXP) [with T = int; SEXP = SEXPREC*]':
compute_cordist.cpp:142:73: required from here
compute_cordist.cpp:119:35: 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, SEXP) [with T = double; SEXP = SEXPREC*]':
compute_cordist.cpp:144:76: required from here
compute_cordist.cpp:119:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
compute_cordist.cpp: In instantiation of 'void average_ranks(const T*, const matrix_info&, const int*, int, double*) [with T = int]':
compute_cordist.cpp:79:58: required from 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]'
compute_cordist.cpp:142:73: required from here
compute_cordist.cpp:12:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:25:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:29:18: 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:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp: In instantiation of 'void average_ranks(const T*, const matrix_info&, const int*, int, double*) [with T = double]':
compute_cordist.cpp:79:58: required from 'SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]'
compute_cordist.cpp:144:76: required from here
compute_cordist.cpp:12:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:25:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:29:18: 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:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<subset_len; ++s) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c compute_rho.cpp -o compute_rho.o
compute_rho.cpp: In function 'SEXPREC* combine_corP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
compute_rho.cpp:421:31: warning: unused variable 'temp_abs_rho' [-Wunused-variable]
double temp_combined, temp_abs_rho;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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˜1.5-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˜1.5-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˜1.5-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˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c overlap_exprs.cpp -o overlap_exprs.o
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, T) [with T = int; SEXP = SEXPREC*]':
overlap_exprs.cpp:138:96: required from here
overlap_exprs.cpp:26:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (cursource[j]<1 || cursource[j]>ncells) {
^
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, T) [with T = double; SEXP = SEXPREC*]':
overlap_exprs.cpp:140:96: required from here
overlap_exprs.cpp:26:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-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˜1.5-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 build_snn.o compute_CV2.o compute_cordist.o compute_rho.o estimate_variance.o forge_system.o init.o matrix_info.o overlap_exprs.o run_dormqr.o shuffle_scores.o -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/scran.buildbin-libdir/scran/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scran' as scran_1.4.5.zip
* DONE (scran)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'scran' successfully unpacked and MD5 sums checked