BioC 3.4: CHECK report for scater on zin1

Package: scater

Version: 1.1.14

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.1.14.tar.gz

StartedAt: 2016-09-20 12:17:49 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:20:44 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 175.4 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_1.1.14.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/scater.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.14’
* 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 5.94  0.004   5.959
* 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) [with T = int; SEXP = SEXPREC*]’:
utils.cpp:277:66:   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:223:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (tptr[0] < 1 || tptr[ntop-1] > MAT.nrow)) {
                                              ^
utils.cpp:234:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:254:24: 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) [with T = double; SEXP = SEXPREC*]’:
utils.cpp:279:69:   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:223:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (tptr[0] < 1 || tptr[ntop-1] > MAT.nrow)) {
                                              ^
utils.cpp:234:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:254:24: 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’
Creating a generic function for ‘plot’ from package ‘graphics’ 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	0.596	0.008	0.605
bootstraps	0.284	0.004	0.288
calcIsExprs	0.5	0.0	0.5
calculateFPKM	0.364	0.000	0.364
calculateQCMetrics	0.38	0.00	0.38
calculateTPM	0.56	0.00	0.56
cellNames	0.276	0.000	0.275
cellPairwiseDistances	0.284	0.000	0.283
counts	0.372	0.104	0.474
cpm	0.272	0.000	0.273
fData	0	0	0
featurePairwiseDistances	0.276	0.004	0.281
filter	0.364	0.000	0.361
findImportantPCs	1.016	0.000	1.018
fpkm	0.436	0.000	0.432
fromCellDataSet	1.236	0.016	1.252
getBMFeatureAnnos	0	0	0
getExprs	0.580	0.012	0.590
get_exprs	0.472	0.116	0.588
isOutlier	0.36	0.00	0.36
is_exprs	0.288	0.004	0.289
multiplot	1.260	0.004	1.266
mutate	0.284	0.020	0.304
newSCESet	0.288	0.008	0.295
nexprs	0.280	0.000	0.281
norm_counts	0.284	0.000	0.285
norm_cpm	0.304	0.000	0.303
norm_exprs	0.3	0.0	0.3
norm_fpkm	0.28	0.00	0.28
norm_tpm	0.304	0.000	0.304
normaliseExprs	1.320	0.000	1.321
normalize	1.404	0.000	1.405
pData	0	0	0
plot	3.680	0.008	3.688
plotDiffusionMap	3.540	0.020	3.576
plotExplanatoryVariables	0.876	0.004	0.883
plotExpression	5.940	0.004	5.959
plotExprsFreqVsMean	1.440	0.000	1.439
plotFeatureData	1.052	0.000	1.051
plotHighestExprs	1.008	0.004	1.012
plotMDS	1.596	0.004	1.598
plotMetadata	0.500	0.000	0.501
plotPCA	4.896	0.008	4.916
plotPhenoData	0.608	0.000	0.606
plotQC	2.060	0.004	2.066
plotReducedDim	2.976	0.004	2.980
plotTSNE	3.084	0.000	3.093
readKallistoResults	0	0	0
readKallistoResultsOneSample	0	0	0
readSalmonResults	0.000	0.000	0.001
readSalmonResultsOneSample	0	0	0
readTxResults	0.000	0.000	0.001
reducedDimension	0.284	0.000	0.284
rename	0.312	0.000	0.314
runKallisto	0.000	0.000	0.001
scater_gui	0.764	0.000	0.764
set_exprs	0.368	0.000	0.366
sizeFactors	0.512	0.000	0.510
stand_exprs	0.264	0.000	0.265
summariseExprsAcrossFeatures	1.372	0.000	1.369
toCellDataSet	0.480	0.004	0.482
tpm	0.332	0.000	0.334
updateSCESet	0.484	0.000	0.487