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BioC 3.4: INSTALL report for scater on malbec1

This page was generated on 2017-04-15 16:13:33 -0400 (Sat, 15 Apr 2017).

Package 1114/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.2.0
Davis McCarthy
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/scater
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: 1.2.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL scater
StartedAt: 2017-04-14 18:08:58 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 18:09:10 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 12.9 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL scater
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.4-bioc/R/library’
* installing *source* package ‘scater’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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) { 
                                                      ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix_info.cpp -o matrix_info.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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, SEXP) [with T = int; SEXP = SEXPREC*]’:
utils.cpp:298:74:   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:235:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (sptr[s] < 0 || sptr[s] >= MAT.nrow) { 
                                        ^
utils.cpp:254:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:265:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (r=0; r<itercycles; ++r) {
                        ^
utils.cpp:275:24: 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:300:77:   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:235:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (sptr[s] < 0 || sptr[s] >= MAT.nrow) { 
                                        ^
utils.cpp:254:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:265:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (r=0; r<itercycles; ++r) {
                        ^
utils.cpp:275:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (t=0; t<ntop; ++t) {
                        ^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o scater.so calc_cpm.o init.o matrix_info.o utils.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/R/library/scater/libs
** 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
* DONE (scater)