BioC 3.5: CHECK report for scran on malbec2

Package: scran

Version: 1.4.5

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scran_1.4.5.tar.gz

StartedAt: 2017-08-16 02:09:59 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:13:58 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 239.6 seconds

RetCode: 0

Status:  OK

CheckDir: scran.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scran_1.4.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/scran.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.4.5’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scran’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘scran’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c build_snn.cpp -o build_snn.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_CV2.cpp -o compute_CV2.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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:79:22:   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:79:22:   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) {
                    ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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;
                               ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c estimate_variance.cpp -o estimate_variance.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c forge_system.cpp -o forge_system.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++  -I/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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]
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c run_dormqr.cpp -o run_dormqr.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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]
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o scran.so 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 -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/scran.Rcheck/scran/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scran)

name	user	system	elapsed
DM	0.128	0.000	0.128
buildSNNGraph	0.132	0.000	0.130
combineVar	4.064	0.036	4.105
computeSpikeFactors	1.064	0.000	1.068
computeSumFactors	2.184	0.004	2.187
convertTo	4.196	0.032	4.233
correlatePairs	0.156	0.000	0.156
cyclone	0.320	0.000	0.322
decomposeVar	1.816	0.000	1.818
denoisePCA	0.172	0.000	0.171
exploreData	0.972	0.000	1.047
findMarkers	2.116	0.000	2.128
improvedCV2	1.172	0.024	1.200
mnnCorrect	0.084	0.004	0.086
overlapExprs	0.868	0.004	0.875
quickCluster	0.508	0.000	0.510
sandbag	0.104	0.000	0.104
selectorPlot	0.448	0.000	0.445
spikes	0.936	0.000	0.938
technicalCV2	1.560	0.012	1.575
testVar	0.036	0.000	0.037
trendVar	1.672	0.000	1.675