RnBeads.hg19 1.0.0
Fabian Mueller
| Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/RnBeads.hg19 | | Last Changed Rev: 3279 / Revision: 3442 | | Last Changed Date: 2015-04-16 13:16:53 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | TIMEOUT | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | TIMEOUT | OK | |
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### Running command:
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### rm -rf RnBeads.hg19.buildbin-libdir RnBeads.hg19.Rcheck && mkdir RnBeads.hg19.buildbin-libdir RnBeads.hg19.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RnBeads.hg19.buildbin-libdir RnBeads.hg19_1.0.0.tar.gz >RnBeads.hg19.Rcheck\00install.out 2>&1 && cp RnBeads.hg19.Rcheck\00install.out RnBeads.hg19-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RnBeads.hg19.buildbin-libdir --install="check:RnBeads.hg19-install.out" --force-multiarch --no-vignettes --timings RnBeads.hg19_1.0.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-data-experiment/meat/RnBeads.hg19.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RnBeads.hg19/DESCRIPTION' ... OK
* this is package 'RnBeads.hg19' version '1.0.0'
* 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 whether package 'RnBeads.hg19' can be installed ... OK
* checking installed package size ... NOTE
installed size is 114.0Mb
sub-directories of 1Mb or more:
data 113.9Mb
* 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
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'GenomicRanges'
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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'hg19.Rd':
'rnb.get.assemblies' 'rnb.get.chromosomes' 'rnb.get.annotation'
'rnb.set.annotation' 'rnb.get.mapping' 'rnb.annotation.size'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented data sets:
'sites' 'regions' 'rnb.set.example'
All user-level objects in a package 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 ... NOTE
Error : .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
call: initialize(value, ...)
error: attempt to apply non-function
Failed with error: 'package 'TxDb.Hsapiens.UCSC.hg19.knownGene' could not be loaded'
Error in .requirePackage(package) :
unable to find required package 'RnBeads'
Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
Execution halted
* 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
hg19.CpG.RData 96.2Mb 59.9Mb xz
hg19.probes27.RData 1.3Mb 809Kb xz
hg19.probes450.RData 9.5Mb 6.2Mb xz
hg19.regions.RData 6.4Mb 2.5Mb xz
small.example.object.RData 545Kb 361Kb xz
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 4 NOTEs
See
'E:/biocbld/bbs-3.1-data-experiment/meat/RnBeads.hg19.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'RnBeads.hg19' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'RnBeads.hg19' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'RnBeads.hg19' as RnBeads.hg19_1.0.0.zip
* DONE (RnBeads.hg19)