Laurent Gatto
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Pbase |
| Branch: RELEASE_3_10 |
| Last Commit: fffa65a |
| Last Changed Date: 2019-10-29 13:09:00 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:23:11 -0400 (Wed, 15 Apr 2020).
| Package 1233/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Laurent Gatto
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: Pbase |
| Version: 0.26.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Pbase_0.26.0.tar.gz |
| StartedAt: 2020-04-15 05:22:27 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:34:05 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 697.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Pbase.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Pbase_0.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Pbase.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 'Pbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pbase' version '0.26.0'
* 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 'Pbase' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcD4MKv/R.INSTALL26d83a3d75ef/Pbase/man/Proteins-class.Rd:121: file link 'proteins' in package 'ensembldb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcD4MKv/R.INSTALL26d83a3d75ef/Pbase/man/Proteins-class.Rd:126: file link 'listColumns' in package 'ensembldb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcD4MKv/R.INSTALL26d83a3d75ef/Pbase/man/Proteins-class.Rd:232: file link 'cleave' in package 'cleaver' does not exist and so has been treated as a topic
Warning: Package 'Pbase' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Pbase.Rcheck/00install.out' for details.
* 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
Proteins-class 11.03 1.26 14.33
etrid2grl 1.08 0.10 5.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Proteins-class 13.72 0.39 14.12
etrid2grl 1.86 0.08 7.11
* 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 WARNING
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/Pbase.Rcheck/00check.log'
for details.
Pbase.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/Pbase_0.26.0.tar.gz && rm -rf Pbase.buildbin-libdir && mkdir Pbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pbase.buildbin-libdir Pbase_0.26.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Pbase_0.26.0.zip && rm Pbase_0.26.0.tar.gz Pbase_0.26.0.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 3705k 100 3705k 0 0 27.2M 0 --:--:-- --:--:-- --:--:-- 28.0M
install for i386
* installing *source* package 'Pbase' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Pbase'
finding HTML links ... done
Pparams-class html
Proteins-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcD4MKv/R.INSTALL26d83a3d75ef/Pbase/man/Proteins-class.Rd:121: file link 'proteins' in package 'ensembldb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcD4MKv/R.INSTALL26d83a3d75ef/Pbase/man/Proteins-class.Rd:126: file link 'listColumns' in package 'ensembldb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcD4MKv/R.INSTALL26d83a3d75ef/Pbase/man/Proteins-class.Rd:232: file link 'cleave' in package 'cleaver' does not exist and so has been treated as a topic
calculateHeavyLabels html
etrid2grl html
isReverse html
p html
plotAsAnnotationTrack html
proteinCoding-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'Pbase' is deprecated and will be removed from Bioconductor
version 3.11
** testing if installed package can be loaded from final location
Warning: Package 'Pbase' is deprecated and will be removed from Bioconductor
version 3.11
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Pbase' ...
** testing if installed package can be loaded
Warning: Package 'Pbase' is deprecated and will be removed from Bioconductor
version 3.11
* MD5 sums
packaged installation of 'Pbase' as Pbase_0.26.0.zip
* DONE (Pbase)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Pbase' successfully unpacked and MD5 sums checked
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Pbase.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.
> library("testthat")
> test_check("Pbase")
Loading required package: Pbase
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: Rcpp
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
== testthat results ===========================================================
[ OK: 170 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
Package 'Pbase' is deprecated and will be removed from Bioconductor
version 3.11
>
> proc.time()
user system elapsed
22.78 4.75 82.82
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Pbase.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.
> library("testthat")
> test_check("Pbase")
Loading required package: Pbase
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: Rcpp
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
== testthat results ===========================================================
[ OK: 170 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
Package 'Pbase' is deprecated and will be removed from Bioconductor
version 3.11
>
> proc.time()
user system elapsed
28.21 2.62 30.82
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Pbase.Rcheck/examples_i386/Pbase-Ex.timings
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Pbase.Rcheck/examples_x64/Pbase-Ex.timings
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