scater 1.4.0 Davis McCarthy
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | URL: https://git.bioconductor.org/packages/scater | Branch: RELEASE_3_5 | Last Commit: 90a2eab | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/scater.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.4.0’
* 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 ‘scater’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.6Mb
sub-directories of 1Mb or more:
doc 5.6Mb
* 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 ... NOTE
S3 methods shown with full name in documentation object 'arrange':
‘arrange.SCESet’
S3 methods shown with full name in documentation object 'filter':
‘filter.SCESet’
S3 methods shown with full name in documentation object 'mutate':
‘mutate.SCESet’
S3 methods shown with full name in documentation object 'rename':
‘rename.SCESet’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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
plotExpression 7.504 0.004 7.611
plotPCA 5.944 0.008 5.957
plotReducedDim 5.836 0.004 5.856
plotRLE 5.736 0.020 5.763
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/scater.Rcheck/00check.log’
for details.
* installing *source* package ‘scater’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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]
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 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) {
^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o scater.so calc_exprs.o init.o matrix_info.o utils.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/scater.Rcheck/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)