Philip Lijnzaad
| Snapshot Date: 2019-10-17 09:00:12 -0400 (Thu, 17 Oct 2019) |
| URL: https://git.bioconductor.org/packages/dyebiasexamples |
| Branch: RELEASE_3_9 |
| Last Commit: 681955d |
| Last Changed Date: 2019-05-02 11:56:20 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 experimental data |
This page was generated on 2019-10-17 16:51:22 -0400 (Thu, 17 Oct 2019).
| Package 101/371 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| dyebiasexamples 1.24.0 Philip Lijnzaad
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |
| Package: dyebiasexamples |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dyebiasexamples.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dyebiasexamples_1.24.0.tar.gz |
| StartedAt: 2019-10-17 13:06:41 -0400 (Thu, 17 Oct 2019) |
| EndedAt: 2019-10-17 13:07:38 -0400 (Thu, 17 Oct 2019) |
| EllapsedTime: 56.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: dyebiasexamples.Rcheck |
| Warnings: 5 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dyebiasexamples.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dyebiasexamples_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/dyebiasexamples.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebiasexamples/DESCRIPTION’ ... OK
* this is package ‘dyebiasexamples’ version ‘1.24.0’
* 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 ‘dyebiasexamples’ can be installed ... WARNING
Found the following significant warnings:
Warning: /home/biocbuild/bbs-3.9-data-experiment/meat/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
Warning: /home/biocbuild/bbs-3.9-data-experiment/meat/dyebiasexamples/man/dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
See ‘/home/biocbuild/bbs-3.9-data-experiment/meat/dyebiasexamples.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 40.3Mb
sub-directories of 1Mb or more:
data 5.3Mb
extradata 34.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
* 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
Packages in Depends field not imported from:
‘GEOquery’ ‘marray’
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
.extract.measurements: no visible global function definition for
‘GSMList’
.extract.measurements : : no visible global function
definition for ‘Table’
.extract.meta: no visible global function definition for ‘GSMList’
.extract.meta : : no visible global function definition for
‘Meta’
.gsmlist2targetinfo: no visible global function definition for
‘GSMList’
.gsmlist2targetinfo: no visible global function definition for ‘Meta’
.have.umcu.version: no visible global function definition for
‘package.version’
dyebias.geo2marray: no visible global function definition for ‘GSMList’
dyebias.geo2marray : : no visible global function definition
for ‘Meta’
dyebias.geo2marray: no visible global function definition for ‘Meta’
dyebias.geo2marray: no visible global function definition for ‘GPLList’
dyebias.geo2marray: no visible global function definition for ‘Table’
dyebias.geo2marray: no visible global function definition for
‘read.marrayLayout’
dyebias.geo2marray: no visible global function definition for
‘Accession’
dyebias.geo2marray: no visible global function definition for
‘maControls<-’
dyebias.geo2marray: no visible global function definition for ‘new’
dyebias.geo2marray: no visible global function definition for
‘maLabels<-’
dyebias.geo2marray: no visible global function definition for
‘maInfo<-’
dyebias.geo2marray: no visible global function definition for ‘maRf’
dyebias.geo2marray: no visible global function definition for ‘maRb<-’
dyebias.geo2marray: no visible global function definition for ‘maGb<-’
dyebias.geo2marray: no visible global function definition for
‘maTargets<-’
dyebias.geo2marray: no visible global function definition for
‘maLayout<-’
dyebias.geo2marray: no visible global function definition for
‘maGnames<-’
Undefined global functions or variables:
Accession GPLList GSMList Meta Table maControls<- maGb<- maGnames<-
maInfo<- maLabels<- maLayout<- maRb<- maRf maTargets<- new
package.version read.marrayLayout
Consider adding
importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
prepare_Rd: dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
* 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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
‘README’
Please use e.g. ‘inst/extdata’ for non-R data files
* 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
data.norm.rda 2.1Mb 1.5Mb xz
data.raw.rda 3.2Mb 2.2Mb xz
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘ChangeLog’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.9-data-experiment/meat/dyebiasexamples.Rcheck/00check.log’
for details.
dyebiasexamples.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL dyebiasexamples ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘dyebiasexamples’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help Warning: /home/biocbuild/bbs-3.9-data-experiment/meat/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped Warning: /home/biocbuild/bbs-3.9-data-experiment/meat/dyebiasexamples/man/dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped *** 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 (dyebiasexamples)
dyebiasexamples.Rcheck/dyebiasexamples-Ex.timings
| name | user | system | elapsed | |
| data.raw | 0.444 | 0.000 | 0.444 | |
| dyebias.geo2marray | 0 | 0 | 0 | |
| dyebias.umcu.proper.estimators | 0.944 | 0.016 | 1.001 | |