Audrey Kauffmann
| Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021) |
| URL: https://git.bioconductor.org/packages/CCl4 |
| Branch: RELEASE_3_12 |
| Last Commit: 452a2a5 |
| Last Changed Date: 2020-10-27 09:47:36 -0400 (Tue, 27 Oct 2020) |
| Back to Build/check report for BioC 3.12 experimental data |
|
This page was generated on 2021-05-06 14:10:06 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the CCl4 package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 47/398 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| CCl4 1.28.0 (landing page) Audrey Kauffmann
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | |||||||
| Package: CCl4 |
| Version: 1.28.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CCl4.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CCl4_1.28.0.tar.gz |
| StartedAt: 2021-05-06 11:41:14 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 11:42:34 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 80.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CCl4.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CCl4.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CCl4_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/CCl4.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CCl4/DESCRIPTION’ ... OK
* this is package ‘CCl4’ version ‘1.28.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CCl4’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 304.2Mb
sub-directories of 1Mb or more:
data 12.0Mb
extdata 292.2Mb
* 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 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 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
CCl4.RData 9.1Mb 2.1Mb xz
CCl4_RGList.RData 2.9Mb 2.0Mb xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘validDataFiles.R’
Comparing ‘validDataFiles.Rout’ to ‘validDataFiles.Rout.save’ ...5,25d4
< 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.max, which.min
<
28,37c7,9
< Vignettes contain introductory material; view with
< 'browseVignettes()'. To cite Bioconductor, see
< 'citation("Biobase")', and for packages 'citation("pkgname")'.
<
<
< Attaching package: 'limma'
<
< The following object is masked from 'package:BiocGenerics':
<
< plotMA
---
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
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, 1 NOTE
See
‘/home/biocbuild/bbs-3.12-data-experiment/meat/CCl4.Rcheck/00check.log’
for details.
CCl4.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CCl4 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘CCl4’ ... ** using staged installation ** data ** inst ** help *** installing help indices ** 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 * DONE (CCl4)
CCl4.Rcheck/tests/validDataFiles.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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("CCl4")
Loading required package: Biobase
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.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
> dataPath = system.file("extdata", package="CCl4")
> if(setequal(dir(dataPath),
+ c("251316214319_auto_479-628.gpr", "251316214320_auto_478-629.gpr",
+ "251316214321_auto_410-592.gpr", "251316214329_auto_429-673.gpr",
+ "251316214330_auto_457-658.gpr", "251316214331_auto_431-588.gpr",
+ "251316214332_auto_492-625.gpr", "251316214333_auto_487-712.gpr",
+ "251316214379_auto_443-617.gpr", "251316214380_auto_493-682.gpr",
+ "251316214381_auto_497-602.gpr", "251316214382_auto_481-674.gpr",
+ "251316214384_auto_450-642.gpr", "251316214389_auto_456-694.gpr",
+ "251316214390_auto_456-718.gpr", "251316214391_auto_475-599.gpr",
+ "251316214393_auto_460-575.gpr", "251316214394_auto_463-521.gpr",
+ "samplesInfo.txt", "013162_D_SequenceList_20060815.txt"))) {
+ cat("Fine.\n")
+ } else {
+ cat(sprintf("Contents of %s differs from expectation.\n", dataPath))
+ }
Fine.
>
> proc.time()
user system elapsed
0.736 0.056 0.790
CCl4.Rcheck/tests/validDataFiles.Rout.save
R version 2.9.0 Under development (unstable) (2009-03-06 r48061)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
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("CCl4")
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: limma
> dataPath = system.file("extdata", package="CCl4")
> if(setequal(dir(dataPath),
+ c("251316214319_auto_479-628.gpr", "251316214320_auto_478-629.gpr",
+ "251316214321_auto_410-592.gpr", "251316214329_auto_429-673.gpr",
+ "251316214330_auto_457-658.gpr", "251316214331_auto_431-588.gpr",
+ "251316214332_auto_492-625.gpr", "251316214333_auto_487-712.gpr",
+ "251316214379_auto_443-617.gpr", "251316214380_auto_493-682.gpr",
+ "251316214381_auto_497-602.gpr", "251316214382_auto_481-674.gpr",
+ "251316214384_auto_450-642.gpr", "251316214389_auto_456-694.gpr",
+ "251316214390_auto_456-718.gpr", "251316214391_auto_475-599.gpr",
+ "251316214393_auto_460-575.gpr", "251316214394_auto_463-521.gpr",
+ "samplesInfo.txt", "013162_D_SequenceList_20060815.txt"))) {
+ cat("Fine.\n")
+ } else {
+ cat(sprintf("Contents of %s differs from expectation.\n", dataPath))
+ }
Fine.
>
CCl4.Rcheck/CCl4-Ex.timings
| name | user | system | elapsed | |
| CCl4 | 0.740 | 0.028 | 0.769 | |