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BioC 3.4: INSTALL report for scater on moscato1

This page was generated on 2016-09-21 03:48:01 -0700 (Wed, 21 Sep 2016).

Package 1085/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.1.14
Davis McCarthy
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/scater
Last Changed Rev: 120896 / Revision: 121152
Last Changed Date: 2016-09-13 06:25:03 -0700 (Tue, 13 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scater
Version: 1.1.14
Command: rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/scater_1.1.14.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=scater.buildbin-libdir --merge-multiarch scater_1.1.14.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL scater_1.1.14.zip && rm scater_1.1.14.tar.gz scater_1.1.14.zip
StartedAt: 2016-09-19 21:11:50 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 21:12:35 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 44.4 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/scater_1.1.14.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=scater.buildbin-libdir --merge-multiarch scater_1.1.14.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL scater_1.1.14.zip  && rm scater_1.1.14.tar.gz scater_1.1.14.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
100 4173k  100 4173k    0     0  71.3M      0 --:--:-- --:--:-- --:--:-- 76.9M

install for i386

* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c calc_cpm.cpp -o calc_cpm.o
calc_cpm.cpp: In instantiation of 'SEXPREC* calc_cpm_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]':
calc_cpm.cpp:53:82:   required from here
calc_cpm.cpp:5:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(lib_sizes) || LENGTH(lib_sizes)!=MAT.ncol) { 
                                                ^
calc_cpm.cpp:9:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(prior_counts) || LENGTH(prior_counts)!=MAT.ncol) { 
                                                      ^
calc_cpm.cpp: In instantiation of 'SEXPREC* calc_cpm_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]':
calc_cpm.cpp:55:85:   required from here
calc_cpm.cpp:5:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(lib_sizes) || LENGTH(lib_sizes)!=MAT.ncol) { 
                                                ^
calc_cpm.cpp:9:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(prior_counts) || LENGTH(prior_counts)!=MAT.ncol) { 
                                                      ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/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"D:/biocbld/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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c utils.cpp -o utils.o
utils.cpp: In instantiation of 'SEXPREC* colsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:56:65:   required from here
utils.cpp:26:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s] < 1 || sptr[s] > MAT.nrow) { 
                                    ^
utils.cpp: In instantiation of 'SEXPREC* colsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]':
utils.cpp:58:68:   required from here
utils.cpp:26:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
utils.cpp: In instantiation of 'SEXPREC* colsum_exprs_subset_internal(const T*, const matrix_info&, T, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:109:93:   required from here
utils.cpp:74:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s] < 1 || sptr[s] > MAT.nrow) { 
                                    ^
utils.cpp: In instantiation of 'SEXPREC* colsum_exprs_subset_internal(const T*, const matrix_info&, T, SEXP) [with T = double; SEXP = SEXPREC*]':
utils.cpp:114:93:   required from here
utils.cpp:74:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
utils.cpp: In instantiation of 'SEXPREC* calc_top_features_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:277:66:   required from here
utils.cpp:218:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:223:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (tptr[0] < 1 || tptr[ntop-1] > MAT.nrow)) {
                                              ^
utils.cpp:234:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:254:24: 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) [with T = double; SEXP = SEXPREC*]':
utils.cpp:279:69:   required from here
utils.cpp:218:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:223:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (tptr[0] < 1 || tptr[ntop-1] > MAT.nrow)) {
                                              ^
utils.cpp:234:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:254:24: 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_cpm.o init.o matrix_info.o utils.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-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'
Creating a generic function for 'plot' from package 'graphics' 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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c calc_cpm.cpp -o calc_cpm.o
calc_cpm.cpp: In instantiation of 'SEXPREC* calc_cpm_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]':
calc_cpm.cpp:53:82:   required from here
calc_cpm.cpp:5:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(lib_sizes) || LENGTH(lib_sizes)!=MAT.ncol) { 
                                                ^
calc_cpm.cpp:9:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(prior_counts) || LENGTH(prior_counts)!=MAT.ncol) { 
                                                      ^
calc_cpm.cpp: In instantiation of 'SEXPREC* calc_cpm_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]':
calc_cpm.cpp:55:85:   required from here
calc_cpm.cpp:5:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(lib_sizes) || LENGTH(lib_sizes)!=MAT.ncol) { 
                                                ^
calc_cpm.cpp:9:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(prior_counts) || LENGTH(prior_counts)!=MAT.ncol) { 
                                                      ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/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"D:/biocbld/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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c utils.cpp -o utils.o
utils.cpp: In instantiation of 'SEXPREC* colsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:56:65:   required from here
utils.cpp:26:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s] < 1 || sptr[s] > MAT.nrow) { 
                                    ^
utils.cpp: In instantiation of 'SEXPREC* colsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]':
utils.cpp:58:68:   required from here
utils.cpp:26:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
utils.cpp: In instantiation of 'SEXPREC* colsum_exprs_subset_internal(const T*, const matrix_info&, T, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:109:93:   required from here
utils.cpp:74:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s] < 1 || sptr[s] > MAT.nrow) { 
                                    ^
utils.cpp: In instantiation of 'SEXPREC* colsum_exprs_subset_internal(const T*, const matrix_info&, T, SEXP) [with T = double; SEXP = SEXPREC*]':
utils.cpp:114:93:   required from here
utils.cpp:74:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
utils.cpp: In instantiation of 'SEXPREC* calc_top_features_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]':
utils.cpp:277:66:   required from here
utils.cpp:218:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:223:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (tptr[0] < 1 || tptr[ntop-1] > MAT.nrow)) {
                                              ^
utils.cpp:234:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:254:24: 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) [with T = double; SEXP = SEXPREC*]':
utils.cpp:279:69:   required from here
utils.cpp:218:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:223:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (tptr[0] < 1 || tptr[ntop-1] > MAT.nrow)) {
                                              ^
utils.cpp:234:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:254:24: 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_cpm.o init.o matrix_info.o utils.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.1.14.zip
* DONE (scater)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'scater' successfully unpacked and MD5 sums checked