Package: PharmacoGx

Version: 1.8.3

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PharmacoGx_1.8.3.tar.gz

StartedAt: 2018-04-12 01:46:45 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:48:40 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 114.4 seconds

RetCode: 0

Status:  OK

CheckDir: PharmacoGx.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PharmacoGx_1.8.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/PharmacoGx.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PharmacoGx’ version ‘1.8.3’
* package encoding: UTF-8
* 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 ‘PharmacoGx’ 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 loading without being on the library search path ... 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 ... NOTE
  Note: found 2251 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/PharmacoGx.Rcheck/00check.log’
for details.

* installing *source* package ‘PharmacoGx’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PharmacoGx)

name	user	system	elapsed
LogLogisticRegression	0.712	0.008	0.720
PharmacoSet	0.012	0.004	0.018
amcc	1.040	0.004	1.048
availablePSets	0	0	0
cellInfo-set	1.096	0.012	1.108
cellInfo	1.264	0.032	1.298
cellNames-set	1.184	0.004	1.185
cellNames	1.116	0.036	1.153
checkPSetStructure	1.144	0.004	1.148
computeABC	0.724	0.012	0.735
computeAUC	0.460	0.000	0.462
computeAmax	0.436	0.000	0.434
computeICn	1.004	0.000	1.002
computeSlope	0.000	0.000	0.001
connectivityScore	0.048	0.000	0.045
cosinePerm	0.056	0.000	0.057
dateCreated	1.016	0.016	1.032
downloadPSet	0.000	0.000	0.001
downloadPertSig	0	0	0
drugDoseResponseCurve	0.004	0.000	0.000
drugInfo-set	1.032	0.004	1.038
drugInfo	1.000	0.020	1.019
drugNames-set	1.180	0.000	1.182
drugNames	1.104	0.020	1.123
drugPerturbationSig	2.176	0.048	2.240
drugSensitivitySig	1.160	0.024	1.194
fNames	1.148	0.040	1.189
featureInfo-set	1.144	0.016	1.159
featureInfo	1.172	0.020	1.192
filterNoisyCurves	0.752	0.004	0.754
gwc	1.224	0.016	1.240
intersectList	0.000	0.000	0.001
intersectPSet	1.488	0.008	1.496
mDataNames	1.168	0.012	1.181
mcc	2.036	0.000	2.042
molecularProfiles-set	1.204	0.016	1.221
molecularProfiles	1.520	0.144	1.665
pSetName	1.168	0.020	1.191
pertNumber-set	1.224	0.008	1.233
pertNumber	1.212	0.012	1.226
phenoInfo-set	1.124	0.028	1.155
phenoInfo	1.492	0.104	1.597
sensNumber-set	1.152	0.016	1.168
sensNumber	1.204	0.064	1.271
sensitivityInfo-set	1.192	0.008	1.198
sensitivityInfo	1.668	0.160	1.830
sensitivityMeasures	1.148	0.020	1.169
sensitivityProfiles-set	1.144	0.004	1.148
sensitivityProfiles	1.516	0.136	1.652
show-PharmacoSet-method	1.168	0.012	1.181
show-PharmacoSig-method	1.396	0.044	1.450
showSigAnnot	0.968	0.048	1.022
subsetTo	1.184	0.032	1.219
summarizeMolecularProfiles	0.140	0.000	0.143
summarizeSensitivityProfiles	0.048	0.000	0.050
symSetDiffList	0.004	0.000	0.001
unionList	0	0	0