dyebiasexamples 1.9.0
Philip Lijnzaad
| Snapshot Date: 2015-11-25 07:17:28 -0800 (Wed, 25 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/dyebiasexamples | | Last Changed Rev: 3462 / Revision: 3504 | | Last Changed Date: 2015-10-13 13:20:35 -0700 (Tue, 13 Oct 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dyebiasexamples_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/dyebiasexamples.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebiasexamples/DESCRIPTION’ ... OK
* this is package ‘dyebiasexamples’ version ‘1.9.0’
* 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 ... [3s/9s] WARNING
Found the following significant warnings:
Warning: /Users/biocbuild/bbs-3.3-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-3.3-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 ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/dyebiasexamples.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 40.2Mb
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
‘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<-
package.version read.marrayLayout
* 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’ ... OK
* checking examples ... [3s/8s] OK
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.3-data-experiment/meat/dyebiasexamples.Rcheck/00check.log’
for details.
* installing *source* package ‘dyebiasexamples’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
Warning: /Users/biocbuild/bbs-3.3-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-3.3-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)