Nicholas Clark
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/GRmetrics |
| Branch: RELEASE_3_10 |
| Last Commit: 799d154 |
| Last Changed Date: 2020-04-12 21:49:19 -0400 (Sun, 12 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:27:07 -0400 (Wed, 15 Apr 2020).
| Package 747/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GRmetrics 1.12.2 Nicholas Clark
| 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: GRmetrics |
| Version: 1.12.2 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GRmetrics.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GRmetrics_1.12.2.tar.gz |
| StartedAt: 2020-04-15 03:43:33 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:47:31 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 237.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GRmetrics.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GRmetrics.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GRmetrics_1.12.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GRmetrics.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 'GRmetrics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GRmetrics' version '1.12.2'
* 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 'GRmetrics' 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 ... NOTE
Package in Depends field not imported from: 'SummarizedExperiment'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GRlogisticFit: no visible binding for global variable 'experiment'
GRdrawDRC: no visible binding for global variable 'GRvalue'
Undefined global functions or variables:
GRvalue experiment
* 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
GRfit 10.13 0.09 10.22
GRscatter 5.92 0.02 6.71
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GRfit 8.79 0.06 8.85
GRscatter 4.80 0.05 5.40
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.R'
OK
** running tests for arch 'x64' ...
Running 'test.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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/GRmetrics.Rcheck/00check.log'
for details.
GRmetrics.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/GRmetrics_1.12.2.tar.gz && rm -rf GRmetrics.buildbin-libdir && mkdir GRmetrics.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GRmetrics.buildbin-libdir GRmetrics_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GRmetrics_1.12.2.zip && rm GRmetrics_1.12.2.tar.gz GRmetrics_1.12.2.zip
###
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% 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 35847 100 35847 0 0 995k 0 --:--:-- --:--:-- --:--:-- 1129k
install for i386
* installing *source* package 'GRmetrics' ...
** 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 'GRmetrics'
finding HTML links ... done
GRbox html
GRdrawDRC html
GRfit html
finding level-2 HTML links ... done
GRgetDefs html
GRgetGroupVars html
GRgetMetrics html
GRgetValues html
GRscatter html
inputCaseA html
inputCaseC 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 'GRmetrics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GRmetrics' as GRmetrics_1.12.2.zip
* DONE (GRmetrics)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GRmetrics' successfully unpacked and MD5 sums checked
|
GRmetrics.Rcheck/tests_i386/test.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.
> # Case C (example 4) test
> #install.packages('readr') # un-comment and install these packages if necessary
> #install.packages('devtools') # un-comment and install these packages if necessary
> ## try http:// if https:// URLs are not supported
> #if (!requireNamespace("BiocManager", quietly=TRUE))
> #install.packages("BiocManager")
> #BiocManager::install("SummarizedExperiment")
>
> # Load GRmetrics functions
> library(GRmetrics)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
> # Load Case C (example 4) input
> data("inputCaseC")
> # Run GRfit function with case = "C"
> output4 = GRfit(inputData = inputCaseC, groupingVariables = c('cell_line','agent', 'perturbation','replicate', 'time'), case = "C")
There were 50 or more warnings (use warnings() to see the first 50)
>
> # Load Case A (example 1) input
> data("inputCaseA")
> # Run GRfit function with case = "A"
> output1 = GRfit(inputData = inputCaseA, groupingVariables = c('cell_line','agent', 'perturbation','replicate', 'time'), case = "A")
There were 50 or more warnings (use warnings() to see the first 50)
>
> # change type integer to numeric for the sake of testing
> metadata(output1)[[1]]$replicate = as.numeric(metadata(output1)[[1]]$replicate)
> all.equal(output1, output4)
[1] "Attributes: < Component \"metadata\": Component 1: Attributes: < Component \"class\": Lengths (3, 1) differ (string compare on first 1) > >"
[2] "Attributes: < Component \"metadata\": Component 1: Attributes: < Component \"class\": 1 string mismatch > >"
> #[1] TRUE
> # Test passed - output from Case C matches output from Case A
>
> proc.time()
user system elapsed
19.87 0.92 20.78
|
GRmetrics.Rcheck/tests_x64/test.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.
> # Case C (example 4) test
> #install.packages('readr') # un-comment and install these packages if necessary
> #install.packages('devtools') # un-comment and install these packages if necessary
> ## try http:// if https:// URLs are not supported
> #if (!requireNamespace("BiocManager", quietly=TRUE))
> #install.packages("BiocManager")
> #BiocManager::install("SummarizedExperiment")
>
> # Load GRmetrics functions
> library(GRmetrics)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
> # Load Case C (example 4) input
> data("inputCaseC")
> # Run GRfit function with case = "C"
> output4 = GRfit(inputData = inputCaseC, groupingVariables = c('cell_line','agent', 'perturbation','replicate', 'time'), case = "C")
There were 50 or more warnings (use warnings() to see the first 50)
>
> # Load Case A (example 1) input
> data("inputCaseA")
> # Run GRfit function with case = "A"
> output1 = GRfit(inputData = inputCaseA, groupingVariables = c('cell_line','agent', 'perturbation','replicate', 'time'), case = "A")
There were 50 or more warnings (use warnings() to see the first 50)
>
> # change type integer to numeric for the sake of testing
> metadata(output1)[[1]]$replicate = as.numeric(metadata(output1)[[1]]$replicate)
> all.equal(output1, output4)
[1] "Attributes: < Component \"metadata\": Component 1: Attributes: < Component \"class\": Lengths (3, 1) differ (string compare on first 1) > >"
[2] "Attributes: < Component \"metadata\": Component 1: Attributes: < Component \"class\": 1 string mismatch > >"
> #[1] TRUE
> # Test passed - output from Case C matches output from Case A
>
> proc.time()
user system elapsed
22.59 0.40 22.98
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GRmetrics.Rcheck/examples_i386/GRmetrics-Ex.timings
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GRmetrics.Rcheck/examples_x64/GRmetrics-Ex.timings
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