BioC 3.3: CHECK report for scran on zin2

Package: scran

Version: 1.0.4

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings scran_1.0.4.tar.gz

StartedAt: 2016-10-13 06:36:57 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:40:46 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 228.8 seconds

RetCode: 0

Status:  OK

CheckDir: scran.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings scran_1.0.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/scran.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 ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.0.4’
* 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 ‘scran’ 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 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
computeSumFactors 11.954  0.064  12.026
cyclone            0.140  0.116   6.565
* 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 ‘scran’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c compute_rho.cpp -o compute_rho.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c forge_system.cpp -o forge_system.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c shuffle_scores.cpp -o shuffle_scores.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o scran.so compute_rho.o forge_system.o init.o shuffle_scores.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/scran.Rcheck/scran/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scran)

name	user	system	elapsed
DM	0.112	0.004	0.116
computeSpikeFactors	0.812	0.040	0.852
computeSumFactors	11.954	0.064	12.026
convertTo	3.133	0.020	3.160
correlatePairs	0.236	0.040	2.331
cyclone	0.140	0.116	6.565
decomposeVar	1.373	0.044	1.423
normalize	0.765	0.000	0.764
quickCluster	1.342	0.020	1.363
sandbag	0.097	0.000	0.097
spikes	0.584	0.004	0.589
testVar	0.026	0.000	0.026
trendVar	1.646	0.020	1.667