scran 1.2.2
Aaron Lun
| 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/scran | | Last Changed Rev: 126005 / Revision: 128728 | | Last Changed Date: 2017-01-18 07:52:47 -0500 (Wed, 18 Jan 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings scran_1.2.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/scran.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.2’
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
computeSumFactors 10.640 0.032 10.682
trendVar 5.132 0.016 5.151
* 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-3.4-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-3.4-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) [with T = int; SEXP = SEXPREC*]’:
compute_cordist.cpp:145:59: required from here
compute_cordist.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<slen; ++s) {
^
compute_cordist.cpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sptr[s]<0 || sptr[s]>=MAT.nrow) {
^
compute_cordist.cpp:85:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<slen; ++s) {
^
compute_cordist.cpp:92:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<slen; ++s) {
^
compute_cordist.cpp:117:35: 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) [with T = double; SEXP = SEXPREC*]’:
compute_cordist.cpp:147:62: required from here
compute_cordist.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<slen; ++s) {
^
compute_cordist.cpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sptr[s]<0 || sptr[s]>=MAT.nrow) {
^
compute_cordist.cpp:85:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<slen; ++s) {
^
compute_cordist.cpp:92:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<slen; ++s) {
^
compute_cordist.cpp:117:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<slen; ++s) {
^
compute_cordist.cpp: In instantiation of ‘double** average_ranks(const T*, const matrix_info&, const int*, int) [with T = int]’:
compute_cordist.cpp:78:38: required from ‘SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]’
compute_cordist.cpp:145:59: required from here
compute_cordist.cpp:15:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:30:18: 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: In instantiation of ‘double** average_ranks(const T*, const matrix_info&, const int*, int) [with T = double]’:
compute_cordist.cpp:78:38: required from ‘SEXPREC* cordist_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]’
compute_cordist.cpp:147:62: required from here
compute_cordist.cpp:15:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t s=0; s<subset_len; ++s) {
^
compute_cordist.cpp:30:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (s==subset_len-1 || collected[s].first!=collected[s+1].first) {
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c compute_rho.cpp -o compute_rho.o
g++ -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-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 run_dormqr.cpp -o run_dormqr.o
g++ -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -L/usr/local/lib -o scran.so compute_CV2.o compute_cordist.o compute_rho.o estimate_variance.o forge_system.o init.o matrix_info.o run_dormqr.o shuffle_scores.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)