dyebiasexamples 1.16.0
Philip Lijnzaad
| Snapshot Date: 2017-08-15 09:00:06 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_5/experiment/pkgs/dyebiasexamples | | Last Changed Rev: 4155 / Revision: 4227 | | Last Changed Date: 2017-04-24 16:09:26 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings dyebiasexamples_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/dyebiasexamples.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.16.0’
* 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-3.5-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
Warning: /home/biocbuild/bbs-3.5-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/dyebiasexamples/man/dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
See ‘/home/biocbuild/bbs-3.5-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 : <anonymous>: no visible global function
definition for ‘Table’
.extract.meta: no visible global function definition for ‘GSMList’
.extract.meta : <anonymous>: 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 : <anonymous>: 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-3.5-data-experiment/meat/dyebiasexamples.Rcheck/00check.log’
for details.
* installing *source* package ‘dyebiasexamples’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
Warning: /home/biocbuild/bbs-3.5-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
Warning: /home/biocbuild/bbs-3.5-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/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
* DONE (dyebiasexamples)