BioC 3.4: CHECK report for scater on malbec1

Package: scater

Version: 1.2.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.2.0.tar.gz

StartedAt: 2017-04-15 01:10:04 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:13:36 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 211.7 seconds

RetCode: 0

Status:  OK

CheckDir: scater.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/scater.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 ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.2.0’
* 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 ... 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 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 6.568  0.008   6.588
plotPCA        5.892  0.004   5.899
* 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 ‘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/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)

name	user	system	elapsed
arrange	0.576	0.000	0.575
bootstraps	0.264	0.008	0.271
calcIsExprs	0.516	0.000	0.515
calculateFPKM	0.516	0.000	0.518
calculateQCMetrics	0.436	0.000	0.437
calculateTPM	0.532	0.000	0.532
cellNames	0.660	0.004	0.664
cellPairwiseDistances	0.488	0.000	0.489
counts	0.400	0.084	0.486
cpm	0.324	0.000	0.322
fData	0.000	0.000	0.001
featurePairwiseDistances	0.288	0.000	0.289
filter	0.444	0.000	0.445
findImportantPCs	1.600	0.004	1.605
fpkm	0.288	0.000	0.293
fromCellDataSet	2.256	0.020	2.277
getBMFeatureAnnos	0	0	0
getExprs	0.628	0.024	0.653
get_exprs	0.540	0.116	0.657
isOutlier	0.768	0.000	0.781
is_exprs	0.288	0.008	0.294
mergeSCESet	2.232	0.008	2.243
multiplot	1.388	0.000	1.389
mutate	0.424	0.000	0.423
newSCESet	0.460	0.004	0.467
nexprs	0.316	0.004	0.320
norm_counts	0.304	0.000	0.302
norm_cpm	0.348	0.000	0.351
norm_exprs	0.288	0.000	0.289
norm_fpkm	0.304	0.000	0.304
norm_tpm	0.312	0.000	0.309
normaliseExprs	1.26	0.00	1.26
normalize	1.608	0.000	1.610
pData	0.000	0.000	0.001
plot	4.204	0.020	4.234
plotDiffusionMap	4.016	0.016	4.036
plotExplanatoryVariables	0.872	0.008	0.878
plotExpression	6.568	0.008	6.588
plotExprsFreqVsMean	1.408	0.000	1.410
plotExprsVsTxLength	2.112	0.008	2.119
plotFeatureData	0.980	0.008	0.987
plotHighestExprs	1.128	0.000	1.129
plotMDS	1.736	0.000	1.737
plotMetadata	0.508	0.000	0.508
plotPCA	5.892	0.004	5.899
plotPhenoData	0.720	0.000	0.717
plotPlatePosition	0.840	0.004	0.845
plotQC	2.436	0.004	2.440
plotReducedDim	3.464	0.000	3.468
plotTSNE	3.336	0.008	3.405
readKallistoResults	0.000	0.000	0.001
readKallistoResultsOneSample	0.000	0.000	0.001
readSalmonResults	0.004	0.000	0.000
readSalmonResultsOneSample	0	0	0
readTxResults	0	0	0
reducedDimension	0.428	0.000	0.427
rename	0.368	0.000	0.365
runKallisto	0.000	0.000	0.001
runSalmon	0	0	0
scater_gui	0.564	0.000	0.566
set_exprs	0.544	0.000	0.546
sizeFactors	0.640	0.000	0.641
stand_exprs	0.300	0.000	0.301
summariseExprsAcrossFeatures	3.568	0.008	3.581
toCellDataSet	0.556	0.000	0.558
tpm	0.304	0.000	0.304
updateSCESet	0.560	0.000	0.561
writeSCESet	0.312	0.000	0.313