Simon Dirmeier
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/perturbatr |
| Branch: RELEASE_3_8 |
| Last Commit: dca80de |
| Last Changed Date: 2019-01-04 13:43:56 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:01 -0400 (Sat, 13 Apr 2019).
| Package 1144/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| perturbatr 1.2.1 Simon Dirmeier
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: perturbatr |
| Version: 1.2.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings perturbatr_1.2.1.tar.gz |
| StartedAt: 2019-04-13 04:29:03 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:43:55 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 891.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: perturbatr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings perturbatr_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/perturbatr.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'perturbatr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'perturbatr' version '1.2.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'perturbatr' 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bootstrap 53.61 17.26 70.87
HMAnalysedPerturbationData-class 7.99 6.60 14.58
NetworkAnalysedPerturbationData-class 7.86 6.25 14.14
diffuse-methods 7.41 3.47 10.87
geneEffects-methods 7.20 2.18 9.39
rnaiscreen 8.47 0.67 9.14
isBootstrapped-methods 7.28 1.32 8.61
modelFit-methods 7.64 0.82 8.45
inference-methods 7.52 0.93 8.44
params-methods 7.84 0.60 8.47
graph-methods 7.96 0.39 8.34
nestedGeneEffects-methods 7.74 0.61 8.34
hm-methods 7.40 0.22 7.63
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bootstrap 52.61 15.76 68.38
NetworkAnalysedPerturbationData-class 7.96 7.96 15.91
HMAnalysedPerturbationData-class 8.03 7.48 15.53
diffuse-methods 6.97 2.48 9.45
rnaiscreen 8.70 0.16 8.86
modelFit-methods 7.62 0.12 7.75
isBootstrapped-methods 7.31 0.10 7.41
graph-methods 7.08 0.09 7.17
inference-methods 7.01 0.14 7.16
nestedGeneEffects-methods 6.93 0.05 6.97
params-methods 6.70 0.08 6.78
hm-methods 6.60 0.09 6.68
geneEffects-methods 6.46 0.08 6.55
* 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: OK
perturbatr.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/perturbatr_1.2.1.tar.gz && rm -rf perturbatr.buildbin-libdir && mkdir perturbatr.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=perturbatr.buildbin-libdir perturbatr_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL perturbatr_1.2.1.zip && rm perturbatr_1.2.1.tar.gz perturbatr_1.2.1.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 3990k 100 3990k 0 0 34.9M 0 --:--:-- --:--:-- --:--:-- 36.0M
install for i386
* installing *source* package 'perturbatr' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'perturbatr'
finding HTML links ... done
HMAnalysedPerturbationData-class html
NetworkAnalysedPerturbationData-class html
PerturbationData-class html
bootstrap html
dataSet-methods html
diffuse-methods html
filter-methods html
geneEffects-methods html
graph-methods html
hm-methods html
inference-methods html
isBootstrapped-methods html
modelFit-methods html
nestedGeneEffects-methods html
params-methods html
perturbatr-package html
plot.NetworkAnalysedPerturbationData html
plot.PerturbationData html
rbind.PerturbationData html
rnaiscreen html
setModelData-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'perturbatr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'perturbatr' as perturbatr_1.2.1.zip
* DONE (perturbatr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'perturbatr' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
perturbatr.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> # perturbatr: analysis of high-throughput gene perturbation screens
> #
> # Copyright (C) 2018 Simon Dirmeier
> #
> # This file is part of perturbatr
> #
> # perturbatr is free software: you can redistribute it and/or modify
> # it under the terms of the GNU General Public License as published by
> # the Free Software Foundation, either version 3 of the License, or
> # (at your option) any later version.
> #
> # perturbatr is distributed in the hope that it will be useful,
> # but WITHOUT ANY WARRANTY; without even the implied warranty of
> # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> # GNU General Public License for more details.
> #
> # You should have received a copy of the GNU General Public License
> # along with perturbatr If not, see <http://www.gnu.org/licenses/>.
>
>
> library(testthat)
> library(perturbatr)
Attaching package: 'perturbatr'
The following object is masked from 'package:stats':
filter
>
> test_check("perturbatr")
== testthat results ===========================================================
OK: 45 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
155.10 33.14 188.25
|
perturbatr.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> # perturbatr: analysis of high-throughput gene perturbation screens
> #
> # Copyright (C) 2018 Simon Dirmeier
> #
> # This file is part of perturbatr
> #
> # perturbatr is free software: you can redistribute it and/or modify
> # it under the terms of the GNU General Public License as published by
> # the Free Software Foundation, either version 3 of the License, or
> # (at your option) any later version.
> #
> # perturbatr is distributed in the hope that it will be useful,
> # but WITHOUT ANY WARRANTY; without even the implied warranty of
> # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> # GNU General Public License for more details.
> #
> # You should have received a copy of the GNU General Public License
> # along with perturbatr If not, see <http://www.gnu.org/licenses/>.
>
>
> library(testthat)
> library(perturbatr)
Attaching package: 'perturbatr'
The following object is masked from 'package:stats':
filter
>
> test_check("perturbatr")
== testthat results ===========================================================
OK: 43 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
142.20 38.29 180.48
|
|
perturbatr.Rcheck/examples_i386/perturbatr-Ex.timings
|
perturbatr.Rcheck/examples_x64/perturbatr-Ex.timings
|