BioC 3.5: CHECK report for scater on tokay2

Package: scater

Version: 1.4.0

Command: rm -rf scater.buildbin-libdir scater.Rcheck && mkdir scater.buildbin-libdir scater.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scater.buildbin-libdir scater_1.4.0.tar.gz >scater.Rcheck\00install.out 2>&1 && cp scater.Rcheck\00install.out scater-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=scater.buildbin-libdir --install="check:scater-install.out" --force-multiarch --no-vignettes --timings scater_1.4.0.tar.gz

StartedAt: 2017-10-18 02:52:04 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:00:40 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 515.3 seconds

RetCode: 0

Status:  OK

CheckDir: scater.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf scater.buildbin-libdir scater.Rcheck && mkdir scater.buildbin-libdir scater.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scater.buildbin-libdir scater_1.4.0.tar.gz >scater.Rcheck\00install.out 2>&1 && cp scater.Rcheck\00install.out scater-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=scater.buildbin-libdir --install="check:scater-install.out" --force-multiarch --no-vignettes --timings scater_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/scater.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'scater' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/scater.buildbin-libdir/scater/libs/i386/scater.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotExpression   8.13   0.05    8.19
plotRLE          7.02   0.22    7.25
plotPCA          6.35   0.03    6.38
plotReducedDim   5.92   0.01    6.00
plotDiffusionMap 4.41   0.05    6.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotExpression   8.28   0.00    8.28
plotDiffusionMap 6.08   0.07    6.50
plotRLE          5.02   0.25    5.27
plotPCA          5.00   0.02    5.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/scater.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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]
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c matrix_info.cpp -o matrix_info.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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) {
                        ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o init.o matrix_info.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/scater.buildbin-libdir/scater/libs/i386
** 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

install for x64

* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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]
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c matrix_info.cpp -o matrix_info.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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) {
                        ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o init.o matrix_info.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.4.0.zip
* DONE (scater)

name	user	system	elapsed
areSizeFactorsCentred	0.87	0.02	0.89
arrange	0.46	0.01	0.47
bootstraps	0.24	0.02	0.25
calcAverage	0.26	0.00	0.27
calcIsExprs	0.30	0.00	0.29
calculateCPM	0.29	0.00	0.30
calculateFPKM	0.35	0.00	0.34
calculateQCMetrics	1.04	0.01	1.07
calculateTPM	0.50	0.02	0.51
cellNames	0.75	0.00	0.75
cellPairwiseDistances	0.22	0.00	0.22
counts	0.33	0.11	0.43
cpm	0.22	0.00	0.22
fData	0	0	0
featureControlInfo	0.23	0.01	0.25
featurePairwiseDistances	0.24	0.02	0.25
filter	0.47	0.02	0.48
findImportantPCs	3.37	0.01	3.39
fpkm	0.25	0.00	0.25
fromCellDataSet	0.81	0.05	1.22
getBMFeatureAnnos	0	0	0
get_exprs	0.52	0.12	0.64
isOutlier	0.34	0.00	0.34
isSpike	0.28	0.00	0.28
is_exprs	0.20	0.02	0.22
mergeSCESet	2.53	0.00	2.53
multiplot	1.95	0.00	1.95
mutate	0.32	0.01	0.33
newSCESet	0.34	0.00	0.34
nexprs	0.36	0.00	0.36
norm_counts	0.37	0.02	0.39
norm_cpm	0.23	0.00	0.24
norm_exprs	0.36	0.02	0.37
norm_fpkm	0.27	0.01	0.29
norm_tpm	0.23	0.00	0.23
normaliseExprs	1.33	0.05	1.37
normalize	1.75	0.05	1.80
pData	0	0	0
plot	4.05	0.01	4.06
plotDiffusionMap	4.41	0.05	6.55
plotExplanatoryVariables	1.54	0.04	1.59
plotExpression	8.13	0.05	8.19
plotExprsFreqVsMean	3.51	0.03	3.54
plotExprsVsTxLength	2.44	0.03	2.47
plotFeatureData	1.13	0.00	1.13
plotHighestExprs	1.54	0.02	1.56
plotMDS	2.49	0.02	2.50
plotMetadata	0.51	0.01	0.53
plotPCA	6.35	0.03	6.38
plotPhenoData	0.67	0.02	0.68
plotPlatePosition	1.28	0.00	1.33
plotQC	2.59	0.03	2.63
plotRLE	7.02	0.22	7.25
plotReducedDim	5.92	0.01	6.00
plotTSNE	4.60	0.05	4.64
read10XResults	0	0	0
readKallistoResults	0	0	0
readKallistoResultsOneSample	0	0	0
readSalmonResults	0	0	0
readSalmonResultsOneSample	0	0	0
readTxResults	0	0	0
reducedDimension	0.25	0.02	0.26
rename	0.32	0.01	0.35
runKallisto	0	0	0
runSalmon	0	0	0
scater_gui	0.56	0.02	0.58
setSpike	0.47	0.00	0.47
set_exprs	0.59	0.01	0.61
sizeFactors	0.93	0.00	0.92
spikes	0.32	0.00	0.33
stand_exprs	0.25	0.00	0.25
summariseExprsAcrossFeatures	2.77	0.08	2.84
toCellDataSet	0.77	0.02	0.78
tpm	0.34	0.00	0.35
updateSCESet	0.64	0.01	0.65
whichSpike	0.52	0.03	0.55
writeSCESet	0.35	0.02	0.38

name	user	system	elapsed
areSizeFactorsCentred	1.52	0.03	1.55
arrange	0.63	0.00	0.62
bootstraps	0.39	0.00	0.39
calcAverage	0.40	0.00	0.41
calcIsExprs	0.58	0.01	0.59
calculateCPM	0.61	0.00	0.61
calculateFPKM	0.5	0.0	0.5
calculateQCMetrics	1	0	1
calculateTPM	1.05	0.02	1.06
cellNames	1.08	0.03	1.11
cellPairwiseDistances	0.99	0.00	0.98
counts	0.64	0.12	0.77
cpm	0.29	0.02	0.31
fData	0	0	0
featureControlInfo	0.38	0.00	0.38
featurePairwiseDistances	0.33	0.00	0.33
filter	0.37	0.00	0.37
findImportantPCs	3.25	0.03	3.28
fpkm	0.28	0.00	0.28
fromCellDataSet	0.60	0.03	0.63
getBMFeatureAnnos	0	0	0
get_exprs	0.47	0.10	0.56
isOutlier	0.33	0.00	0.32
isSpike	0.34	0.01	0.36
is_exprs	0.35	0.00	0.35
mergeSCESet	3.12	0.00	3.12
multiplot	3.00	0.02	3.02
mutate	0.33	0.00	0.33
newSCESet	0.31	0.02	0.33
nexprs	0.66	0.00	0.66
norm_counts	0.27	0.00	0.27
norm_cpm	0.37	0.01	0.39
norm_exprs	0.44	0.02	0.45
norm_fpkm	0.39	0.03	0.42
norm_tpm	0.36	0.00	0.36
normaliseExprs	1.22	0.00	1.22
normalize	1.28	0.00	1.28
pData	0	0	0
plot	4.78	0.06	4.85
plotDiffusionMap	6.08	0.07	6.50
plotExplanatoryVariables	1.67	0.03	1.70
plotExpression	8.28	0.00	8.28
plotExprsFreqVsMean	2.83	0.03	2.86
plotExprsVsTxLength	2.44	0.00	2.44
plotFeatureData	0.91	0.00	0.90
plotHighestExprs	1.04	0.01	1.07
plotMDS	1.33	0.02	1.34
plotMetadata	0.42	0.00	0.42
plotPCA	5.00	0.02	5.02
plotPhenoData	0.50	0.01	0.51
plotPlatePosition	0.80	0.02	0.82
plotQC	2.50	0.01	2.51
plotRLE	5.02	0.25	5.27
plotReducedDim	3.75	0.02	3.76
plotTSNE	2.67	0.01	2.69
read10XResults	0	0	0
readKallistoResults	0	0	0
readKallistoResultsOneSample	0	0	0
readSalmonResults	0	0	0
readSalmonResultsOneSample	0	0	0
readTxResults	0	0	0
reducedDimension	0.23	0.00	0.23
rename	0.24	0.00	0.23
runKallisto	0	0	0
runSalmon	0	0	0
scater_gui	0.42	0.00	0.42
setSpike	0.33	0.00	0.33
set_exprs	0.36	0.00	0.36
sizeFactors	0.40	0.00	0.41
spikes	0.63	0.02	0.64
stand_exprs	0.22	0.00	0.22
summariseExprsAcrossFeatures	1.98	0.06	2.04
toCellDataSet	0.42	0.02	0.44
tpm	0.41	0.00	0.41
updateSCESet	0.50	0.01	0.51
whichSpike	0.31	0.00	0.31
writeSCESet	0.28	0.00	0.29