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BioC 3.5: INSTALL report for scater on tokay2

This page was generated on 2017-08-16 13:25:23 -0400 (Wed, 16 Aug 2017).

Package 1186/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.4.0
Davis McCarthy
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/scater
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scater
Version: 1.4.0
Command: rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/scater_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=scater.buildbin-libdir --merge-multiarch scater_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL scater_1.4.0.zip && rm scater_1.4.0.tar.gz scater_1.4.0.zip
StartedAt: 2017-08-15 18:31:29 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:32:32 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 63.3 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/scater_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=scater.buildbin-libdir --merge-multiarch scater_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL scater_1.4.0.zip  && rm scater_1.4.0.tar.gz scater_1.4.0.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
 39 1837k   39  720k    0     0   605k      0  0:00:03  0:00:01  0:00:02  606k
 69 1837k   69 1283k    0     0   801k      0  0:00:02  0:00:01  0:00:01  802k
100 1837k  100 1837k    0     0  1143k      0  0:00:01  0:00:01 --:--:-- 1143k

install for i386

* installing *source* package 'scater' ...
** 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 calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'SEXPREC* calc_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]':
calc_exprs.cpp:78:95:   required from here
calc_exprs.cpp:5:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(size_fac) || LENGTH(size_fac)!=MAT.ncol) { 
                                              ^
calc_exprs.cpp: In instantiation of 'SEXPREC* calc_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]':
calc_exprs.cpp:80:98:   required from here
calc_exprs.cpp:5:46: 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 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 utils.cpp -o utils.o
utils.cpp: In function 'subset_info process_subset_vector(SEXP, const matrix_info&, bool)':
utils.cpp:20:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s] < 0 || sptr[s] >= upper) { 
                                    ^
utils.cpp: In instantiation of 'SEXPREC* rowsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:106:65:   required from here
utils.cpp:86:13: warning: unused variable 's' [-Wunused-variable]
         int s;
             ^
utils.cpp: In instantiation of 'SEXPREC* rowsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]':
utils.cpp:108:68:   required from here
utils.cpp:86:13: warning: unused variable 's' [-Wunused-variable]
utils.cpp: In instantiation of 'SEXPREC* calc_top_features_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:336:74:   required from here
utils.cpp:263:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:303:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (r=0; r<itercycles; ++r) {
                        ^
utils.cpp:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (t=0; t<ntop; ++t) {
                        ^
utils.cpp: In instantiation of 'SEXPREC* calc_top_features_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]':
utils.cpp:338:77:   required from here
utils.cpp:263:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:303:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (r=0; r<itercycles; ++r) {
                        ^
utils.cpp:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (t=0; t<ntop; ++t) {
                        ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o init.o matrix_info.o utils.o -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/scater.buildbin-libdir/scater/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for 'mutate' in package 'scater'
Creating a new generic function for 'filter' in package 'scater'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'scater' ...
** 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 calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'SEXPREC* calc_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]':
calc_exprs.cpp:78:95:   required from here
calc_exprs.cpp:5:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(size_fac) || LENGTH(size_fac)!=MAT.ncol) { 
                                              ^
calc_exprs.cpp: In instantiation of 'SEXPREC* calc_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]':
calc_exprs.cpp:80:98:   required from here
calc_exprs.cpp:5:46: 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 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 utils.cpp -o utils.o
utils.cpp: In function 'subset_info process_subset_vector(SEXP, const matrix_info&, bool)':
utils.cpp:20:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s] < 0 || sptr[s] >= upper) { 
                                    ^
utils.cpp: In instantiation of 'SEXPREC* rowsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:106:65:   required from here
utils.cpp:86:13: warning: unused variable 's' [-Wunused-variable]
         int s;
             ^
utils.cpp: In instantiation of 'SEXPREC* rowsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]':
utils.cpp:108:68:   required from here
utils.cpp:86:13: warning: unused variable 's' [-Wunused-variable]
utils.cpp: In instantiation of 'SEXPREC* calc_top_features_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:336:74:   required from here
utils.cpp:263:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:303:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (r=0; r<itercycles; ++r) {
                        ^
utils.cpp:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (t=0; t<ntop; ++t) {
                        ^
utils.cpp: In instantiation of 'SEXPREC* calc_top_features_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]':
utils.cpp:338:77:   required from here
utils.cpp:263:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:303:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (r=0; r<itercycles; ++r) {
                        ^
utils.cpp:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (t=0; t<ntop; ++t) {
                        ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o init.o matrix_info.o utils.o -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/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.4.0.zip
* DONE (scater)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'scater' successfully unpacked and MD5 sums checked