yriMulti 0.0.8
VJ Carey
| Snapshot Date: 2016-01-30 07:15:28 -0800 (Sat, 30 Jan 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/yriMulti | | Last Changed Rev: 3585 / Revision: 3585 | | Last Changed Date: 2016-01-30 04:56:10 -0800 (Sat, 30 Jan 2016) |
| 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 | |
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### Running command:
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### rm -rf yriMulti.buildbin-libdir yriMulti.Rcheck && mkdir yriMulti.buildbin-libdir yriMulti.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=yriMulti.buildbin-libdir yriMulti_0.0.8.tar.gz >yriMulti.Rcheck\00install.out 2>&1 && cp yriMulti.Rcheck\00install.out yriMulti-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=yriMulti.buildbin-libdir --install="check:yriMulti-install.out" --force-multiarch --no-vignettes --timings yriMulti_0.0.8.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-data-experiment/meat/yriMulti.Rcheck'
* using R Under development (unstable) (2016-01-24 r69993)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'yriMulti/DESCRIPTION' ... OK
* this is package 'yriMulti' version '0.0.8'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'gQTLBase' 'SummarizedExperiment' 'GenomicRanges' 'Homo.sapiens'
'dsQTL' 'geuvPack'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'yriMulti' can be installed ... OK
* checking installed package size ... NOTE
installed size is 172.3Mb
sub-directories of 1Mb or more:
data 172.2Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
'GenomicRanges' 'Homo.sapiens' 'SummarizedExperiment' 'dsQTL'
'gQTLBase' 'geuvPack'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bindelms: no visible global function definition for 'mcols'
bindelms: no visible global function definition for 'mcols<-'
bindelms: no visible global function definition for 'metadata<-'
checkGenomes: no visible global function definition for 'genome'
mexDF: no visible global function definition for 'mcols'
mexGR: no visible global function definition for 'mcols'
mexGR: no visible global function definition for 'findOverlaps'
mexGR: no visible global function definition for 'rowRanges'
mexGR: no visible global function definition for 'subjectHits'
mexGR : embell: no visible global function definition for 'DataFrame'
mexGR : embell: no visible global function definition for 'assays'
mexGR : embell: no visible global function definition for 'strand'
mexGR : embell: no visible global function definition for 'seqnames'
mexGR: no visible global function definition for 'GRanges'
mexGR: no visible global function definition for 'IRanges'
mexGR: no visible global function definition for 'mcols<-'
mexGR: no visible global function definition for 'seqinfo<-'
mexGR: no visible global function definition for 'seqinfo'
plotEvM: no visible global function definition for 'mcols'
plotEvM: no visible global function definition for 'metadata'
symind: no visible global function definition for 'mcols'
show,mexGR: no visible global function definition for 'mcols'
show,mexGR: no visible global function definition for 'selectSome'
Undefined global functions or variables:
DataFrame GRanges IRanges assays findOverlaps genome mcols mcols<-
metadata metadata<- rowRanges selectSome seqinfo seqinfo<- seqnames
strand subjectHits
* checking Rd files ... NOTE
prepare_Rd: mexGR.Rd:32-34: Dropping empty section \details
prepare_Rd: mexGR.Rd:49-51: Dropping empty section \note
prepare_Rd: mexGR.Rd:46-48: Dropping empty section \author
prepare_Rd: mexGR.Rd:43-45: Dropping empty section \references
prepare_Rd: mexGR.Rd:55-57: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'bindelms' 'checkGenomes' 'mexDF' 'plotEvM' 'symind'
Undocumented data sets:
'banovichSE'
Undocumented S4 classes:
'mexGR'
Undocumented S4 methods:
generic 'show' and siglist 'mexGR'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
banovichSE.rda 172.2Mb 114.9Mb xz
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [32s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mexGR 16.55 0.31 17.57
** running examples for arch 'x64' ... [33s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mexGR 15.67 0.32 16.18
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 6 NOTEs
See
'E:/biocbld/bbs-3.3-data-experiment/meat/yriMulti.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'yriMulti' ...
** R
** data
** preparing package for lazy loading
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
install for x64
* installing *source* package 'yriMulti' ...
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
* MD5 sums
packaged installation of 'yriMulti' as yriMulti_0.0.8.zip
* DONE (yriMulti)