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BioC 3.5: CHECK report for scater on malbec2

This page was generated on 2017-10-18 14:17:28 -0400 (Wed, 18 Oct 2017).

Package 1185/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scater
Version: 1.4.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.4.0.tar.gz
StartedAt: 2017-10-18 02:21:22 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:25:43 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 261.2 seconds
RetCode: 0
Status:  OK 
CheckDir: scater.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* 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.


scater.Rcheck/00install.out:

* 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)

scater.Rcheck/scater-Ex.timings:

nameusersystemelapsed
areSizeFactorsCentred0.8280.0000.830
arrange0.460.000.46
bootstraps0.2440.0000.247
calcAverage0.3040.0000.305
calcIsExprs0.3000.0000.301
calculateCPM0.3200.0000.317
calculateFPKM0.6720.0000.673
calculateQCMetrics0.4880.0160.504
calculateTPM0.4600.0080.470
cellNames0.4960.0120.508
cellPairwiseDistances0.2240.0000.226
counts0.2880.0760.368
cpm0.2120.0040.217
fData000
featureControlInfo0.2560.0000.255
featurePairwiseDistances0.2320.0000.230
filter0.3160.0000.317
findImportantPCs2.2840.0002.283
fpkm0.2560.0000.255
fromCellDataSet0.5120.0040.515
getBMFeatureAnnos000
get_exprs0.6400.1200.761
isOutlier0.4360.0000.434
isSpike0.2720.0040.278
is_exprs0.2560.0040.263
mergeSCESet2.7920.0002.795
multiplot2.1920.0002.194
mutate0.2360.0000.237
newSCESet0.2320.0000.231
nexprs0.2400.0000.242
norm_counts0.2400.0000.237
norm_cpm0.2240.0000.226
norm_exprs0.2320.0000.234
norm_fpkm0.2320.0000.230
norm_tpm0.2280.0000.226
normaliseExprs1.060.001.06
normalize1.0000.0041.006
pData000
plot3.9080.0203.930
plotDiffusionMap4.3360.0124.364
plotExplanatoryVariables0.9440.0080.955
plotExpression7.5040.0047.611
plotExprsFreqVsMean3.0240.0003.027
plotExprsVsTxLength1.8280.0041.833
plotFeatureData1.0080.0001.009
plotHighestExprs1.1920.0001.194
plotMDS1.9560.0041.963
plotMetadata0.5400.0000.544
plotPCA5.9440.0085.957
plotPhenoData1.2480.0001.251
plotPlatePosition0.9520.0000.952
plotQC2.4240.0042.432
plotRLE5.7360.0205.763
plotReducedDim5.8360.0045.856
plotTSNE4.0640.0044.072
read10XResults0.0000.0000.001
readKallistoResults0.0000.0000.001
readKallistoResultsOneSample000
readSalmonResults000
readSalmonResultsOneSample000
readTxResults0.0000.0000.001
reducedDimension0.4120.0000.413
rename0.3160.0000.318
runKallisto000
runSalmon000
scater_gui0.5720.0000.571
setSpike0.3040.0000.303
set_exprs0.4160.0000.418
sizeFactors0.4720.0000.475
spikes0.3000.0000.302
stand_exprs0.2440.0000.244
summariseExprsAcrossFeatures2.5080.0002.510
toCellDataSet0.6600.0040.666
tpm0.3520.0000.348
updateSCESet0.5560.0000.557
whichSpike0.3920.0000.392
writeSCESet0.3520.0000.352