Simon Dirmeier
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/perturbatr |
| Branch: RELEASE_3_10 |
| Last Commit: 7c959ed |
| Last Changed Date: 2019-10-29 13:11:01 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:30:05 -0400 (Wed, 15 Apr 2020).
| Package 1249/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| perturbatr 1.6.0 Simon Dirmeier
| malbec1 | Linux (Ubuntu 18.04.4 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: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings perturbatr_1.6.0.tar.gz |
| StartedAt: 2020-04-15 05:27:44 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:41:43 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 839.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: perturbatr.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:perturbatr.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings perturbatr_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/perturbatr.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.0'
* 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 '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 88.70 33.42 122.13
HMAnalysedPerturbationData-class 8.35 4.43 12.78
NetworkAnalysedPerturbationData-class 6.66 4.07 10.84
diffuse-methods 6.48 3.58 10.07
graph-methods 6.74 3.01 9.75
modelFit-methods 7.40 2.33 9.74
inference-methods 6.72 2.59 9.31
nestedGeneEffects-methods 7.30 1.81 9.11
params-methods 6.76 2.29 9.04
isBootstrapped-methods 6.47 2.17 8.64
geneEffects-methods 5.92 1.91 7.82
hm-methods 5.64 1.86 7.50
rnaiscreen 5.20 2.09 7.30
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bootstrap 69.03 14.38 83.42
HMAnalysedPerturbationData-class 6.51 3.87 10.39
NetworkAnalysedPerturbationData-class 5.18 4.00 9.20
geneEffects-methods 4.95 1.70 6.67
graph-methods 4.97 1.55 6.51
diffuse-methods 5.00 1.25 6.25
hm-methods 4.56 1.67 6.25
rnaiscreen 4.81 1.32 6.14
modelFit-methods 4.53 1.47 6.00
isBootstrapped-methods 4.37 1.61 5.98
nestedGeneEffects-methods 4.72 1.08 5.79
inference-methods 4.08 1.70 5.79
params-methods 4.12 1.51 5.64
* 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
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/perturbatr_1.6.0.tar.gz && rm -rf perturbatr.buildbin-libdir && mkdir perturbatr.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=perturbatr.buildbin-libdir perturbatr_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL perturbatr_1.6.0.zip && rm perturbatr_1.6.0.tar.gz perturbatr_1.6.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
80 3990k 80 3216k 0 0 13.2M 0 --:--:-- --:--:-- --:--:-- 13.3M
100 3990k 100 3990k 0 0 15.9M 0 --:--:-- --:--:-- --:--:-- 16.1M
install for i386
* installing *source* package 'perturbatr' ...
** using staged installation
** 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 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 'perturbatr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'perturbatr' as perturbatr_1.6.0.zip
* DONE (perturbatr)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'perturbatr' successfully unpacked and MD5 sums checked
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perturbatr.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.
> # 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: 41 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
152.87 16.26 169.15
|
perturbatr.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.
> # 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: 41 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
146.62 18.23 165.12
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perturbatr.Rcheck/examples_i386/perturbatr-Ex.timings
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perturbatr.Rcheck/examples_x64/perturbatr-Ex.timings
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