Benjamin Haibe-Kains
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/PharmacoGx |
| Branch: RELEASE_3_11 |
| Last Commit: 528b270 |
| Last Changed Date: 2020-09-03 13:39:48 -0400 (Thu, 03 Sep 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:23 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE PharmacoGx PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1301/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PharmacoGx 2.0.9 Benjamin Haibe-Kains
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: PharmacoGx |
| Version: 2.0.9 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PharmacoGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings PharmacoGx_2.0.9.tar.gz |
| StartedAt: 2020-10-17 06:52:45 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 07:03:08 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 622.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PharmacoGx.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PharmacoGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings PharmacoGx_2.0.9.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/PharmacoGx.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PharmacoGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PharmacoGx' version '2.0.9'
* 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 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PharmacoSet-class 35.16 0.73 35.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PharmacoSet-class 28.54 0.8 29.34
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/PharmacoGx.Rcheck/00check.log'
for details.
PharmacoGx.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/PharmacoGx_2.0.9.tar.gz && rm -rf PharmacoGx.buildbin-libdir && mkdir PharmacoGx.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PharmacoGx.buildbin-libdir PharmacoGx_2.0.9.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL PharmacoGx_2.0.9.zip && rm PharmacoGx_2.0.9.tar.gz PharmacoGx_2.0.9.zip
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install for i386
* installing *source* package 'PharmacoGx' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PharmacoGx'
finding HTML links ... done
CCLEsmall html
CMAPsmall html
GDSCsmall html
HDAC_genes html
PharmacoSet-class html
PharmacoSet html
amcc html
availablePSets html
callingWaterfall html
cellInfo-set-PharmacoSet-data.frame-method
html
checkPsetStructure html
computeABC html
computeAUC html
computeAmax html
computeICn html
computeSlope html
connectivityScore html
cosinePerm html
dim-PharmacoSet-method html
dot-convertPsetMolecularProfilesToSE html
dot-resaveAllExampleDatasets html
dot-validatePsetMolecularProfilesToSEConversion
html
downloadPSet html
downloadPertSig html
drugDoseResponseCurve html
drugInfo-set html
drugInfo html
drugNames-set html
drugNames html
drugPerturbationSig html
drugSensitivitySig html
fNames-set-PharmacoSet-character-character-method
html
filterNoisyCurves html
geneDrugSensitivity html
gwc html
intersectPSet html
logLogisticRegression html
mDataNames-PharmacoSet-method html
mcc html
plot.PharmacoSig html
show-PharmacoSet-method html
show-PharmacoSig-method html
showSigAnnot html
sub-PharmacoSet-ANY-ANY-ANY-method html
subsetTo html
summarizeMolecularProfiles html
summarizeSensitivityProfiles html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'PharmacoGx' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PharmacoGx' as PharmacoGx_2.0.9.zip
* DONE (PharmacoGx)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'PharmacoGx' successfully unpacked and MD5 sums checked
|
PharmacoGx.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.unsetenv("R_TESTS")
>
> library(testthat)
> library(PharmacoGx)
Loading required package: CoreGx
Attaching package: 'PharmacoGx'
The following objects are masked from 'package:CoreGx':
amcc, connectivityScore, cosinePerm, gwc, mcc
>
> test_check("PharmacoGx")
[1] NA 3
[1] 1 2 Inf
[1] NA 3
[1] 1 2 Inf
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[1] 1 1 -1
[1] 0
[1] 0
[,1] [,2] [,3]
lower_bounds 0 0 0
upper_bounds 1 1 -1
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== testthat results ===========================================================
[ OK: 127 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
101.59 3.26 104.87
|
PharmacoGx.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.unsetenv("R_TESTS")
>
> library(testthat)
> library(PharmacoGx)
Loading required package: CoreGx
Attaching package: 'PharmacoGx'
The following objects are masked from 'package:CoreGx':
amcc, connectivityScore, cosinePerm, gwc, mcc
>
> test_check("PharmacoGx")
[1] NA 3
[1] 1 2 Inf
[1] NA 3
[1] 1 2 Inf
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[1] 1 1 -1
[1] 0
[1] 0
[,1] [,2] [,3]
lower_bounds 0 0 0
upper_bounds 1 1 -1
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== testthat results ===========================================================
[ OK: 127 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
90.57 1.25 91.95
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PharmacoGx.Rcheck/examples_i386/PharmacoGx-Ex.timings
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PharmacoGx.Rcheck/examples_x64/PharmacoGx-Ex.timings
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