gene2pathway 2.13.0
Holger Froehlich
| Snapshot Date: 2012-12-30 17:01:06 -0800 (Sun, 30 Dec 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gene2pathway | | Last Changed Rev: 70052 / Revision: 72203 | | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/gene2pathway.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gene2pathway/DESCRIPTION’ ... OK
* this is package ‘gene2pathway’ version ‘2.13.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMC’
* 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 ‘gene2pathway’ can be installed ... WARNING
Found the following significant warnings:
Warning: class "VirtualSOAPClass" is defined (with package slot ‘SSOAP’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
Warning: class "VirtualXMLSchemaClass" is defined (with package slot ‘XMLSchema’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
See ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/gene2pathway.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gene2pathway: no visible global function definition for ‘registerDoMC’
gene2pathway: no visible global function definition for ‘%dopar%’
gene2pathway: no visible global function definition for ‘foreach’
gene2pathway: no visible binding for global variable ‘g’
gene2pathway: no visible binding for global variable ‘p’
gene2pathway.signaltrans: no visible global function definition for
‘registerDoMC’
gene2pathway.signaltrans: no visible global function definition for
‘%dopar%’
gene2pathway.signaltrans: no visible global function definition for
‘foreach’
gene2pathway.signaltrans: no visible binding for global variable ‘p’
getKEGGHierarchy: no visible binding for global variable ‘keggOrthDF’
predict.gene2pathway : testallBag: no visible global function
definition for ‘%dopar%’
predict.gene2pathway : testallBag: no visible global function
definition for ‘foreach’
predict.gene2pathway : testallBag: no visible binding for global
variable ‘m’
predict.gene2pathway: no visible global function definition for
‘registerDoMC’
test.overrepresentation: no visible global function definition for
‘registerDoMC’
test.overrepresentation: no visible global function definition for
‘%dopar%’
test.overrepresentation: no visible global function definition for
‘foreach’
test.overrepresentation: no visible binding for global variable ‘p’
trainallBag: no visible global function definition for ‘registerDoMC’
trainallBag: no visible global function definition for ‘%dopar%’
trainallBag: no visible global function definition for ‘foreach’
* checking Rd files ... OK
* 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 ... 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
classificationModelSignalTrans_dme.rda 184Kb 26Kb xz
classificationModel_dme.rda 1.3Mb 351Kb xz
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/gene2pathway.Rcheck/00check.log’
for details.
* installing *source* package ‘gene2pathway’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: method with signature ‘PrimitiveSOAPType#list’ chosen for function ‘resolve’,
target signature ‘PrimitiveSOAPType#SchemaCollection’.
"SOAPType#SchemaCollection" would also be valid
Warning: class "VirtualSOAPClass" is defined (with package slot ‘SSOAP’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
Warning: class "VirtualXMLSchemaClass" is defined (with package slot ‘XMLSchema’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
Note: method with signature ‘ArrayType#list’ chosen for function ‘resolve’,
target signature ‘ArrayType#SchemaCollection’.
"SimpleSequenceType#SchemaCollection" would also be valid
** help
*** installing help indices
** building package indices
** installing vignettes
‘gene2pathway.Rnw’ using ‘latin1’
** testing if installed package can be loaded
Note: method with signature ‘PrimitiveSOAPType#list’ chosen for function ‘resolve’,
target signature ‘PrimitiveSOAPType#SchemaCollection’.
"SOAPType#SchemaCollection" would also be valid
Warning: class "VirtualSOAPClass" is defined (with package slot ‘SSOAP’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
Warning: class "VirtualXMLSchemaClass" is defined (with package slot ‘XMLSchema’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
Note: method with signature ‘ArrayType#list’ chosen for function ‘resolve’,
target signature ‘ArrayType#SchemaCollection’.
"SimpleSequenceType#SchemaCollection" would also be valid
* DONE (gene2pathway)