Package: PharmacoGx

Version: 1.8.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PharmacoGx_1.8.3.tar.gz

StartedAt: 2018-04-12 07:37:35 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:40:05 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 150.0 seconds

RetCode: 0

Status:  OK

CheckDir: PharmacoGx.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PharmacoGx_1.8.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PharmacoGx.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/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	0.995	0.013	1.026
PharmacoSet	0.007	0.002	0.010
amcc	1.601	0.006	1.671
availablePSets	0.001	0.000	0.001
cellInfo-set	1.358	0.034	1.412
cellInfo	1.935	0.116	2.080
cellNames-set	1.444	0.019	1.481
cellNames	1.424	0.024	1.482
checkPSetStructure	1.428	0.020	1.502
computeABC	1.100	0.013	1.140
computeAUC	0.707	0.001	0.722
computeAmax	0.679	0.001	0.700
computeICn	1.386	0.007	1.419
computeSlope	0.001	0.000	0.002
connectivityScore	0.054	0.002	0.056
cosinePerm	0.087	0.003	0.091
dateCreated	1.361	0.019	1.412
downloadPSet	0.000	0.001	0.001
downloadPertSig	0.001	0.000	0.001
drugDoseResponseCurve	0.001	0.000	0.001
drugInfo-set	1.391	0.019	1.453
drugInfo	1.395	0.019	1.443
drugNames-set	1.447	0.017	1.508
drugNames	1.409	0.017	1.445
drugPerturbationSig	2.761	0.039	2.872
drugSensitivitySig	1.466	0.026	1.522
fNames	1.367	0.017	1.420
featureInfo-set	1.406	0.017	1.452
featureInfo	1.353	0.016	1.414
filterNoisyCurves	1.018	0.015	1.060
gwc	1.408	0.018	1.457
intersectList	0.001	0.000	0.001
intersectPSet	1.771	0.030	1.844
mDataNames	1.438	0.016	1.490
mcc	2.467	0.006	2.519
molecularProfiles-set	1.254	0.019	1.310
molecularProfiles	2.154	0.320	2.520
pSetName	1.271	0.020	1.311
pertNumber-set	1.471	0.019	1.526
pertNumber	1.413	0.018	1.473
phenoInfo-set	1.458	0.017	1.507
phenoInfo	2.950	0.182	3.184
sensNumber-set	1.388	0.015	1.418
sensNumber	1.347	0.104	1.462
sensitivityInfo-set	1.301	0.017	1.332
sensitivityInfo	2.844	0.438	3.329
sensitivityMeasures	1.397	0.018	1.442
sensitivityProfiles-set	1.460	0.018	1.513
sensitivityProfiles	2.368	0.340	2.781
show-PharmacoSet-method	1.480	0.019	1.528
show-PharmacoSig-method	1.654	0.028	1.714
showSigAnnot	1.154	0.028	1.222
subsetTo	1.483	0.017	1.549
summarizeMolecularProfiles	0.165	0.014	0.181
summarizeSensitivityProfiles	0.056	0.014	0.072
symSetDiffList	0.001	0.000	0.001
unionList	0.001	0.000	0.001