VJ Carey
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/vtpnet |
| Branch: master |
| Last Commit: e864b6b |
| Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:05:22 -0400 (Tue, 09 Apr 2019).
| Package 1679/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| vtpnet 0.23.0 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: vtpnet |
| Version: 0.23.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vtpnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings vtpnet_0.23.0.tar.gz |
| StartedAt: 2019-04-09 06:35:12 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:42:09 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 416.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: vtpnet.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vtpnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings vtpnet_0.23.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/vtpnet.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'vtpnet/DESCRIPTION' ... OK
* this is package 'vtpnet' version '0.23.0'
* 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 'vtpnet' can be installed ... OK
* checking installed package size ... NOTE
installed size is 20.0Mb
sub-directories of 1Mb or more:
data 20.0Mb
* checking package directory ... OK
* checking 'build' 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
'library' or 'require' calls to packages already attached by Depends:
'doParallel' 'foreach'
Please remove these calls from your code.
'library' or 'require' call to 'MotifDb' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'doParallel' 'foreach'
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
rng2facHits: warning in dir(patt = "rda$"): partial argument match of
'patt' to 'pattern'
runfimo: warning in dir(patt = "_out"): partial argument match of
'patt' to 'pattern'
filterGWASbyMap: no visible global function definition for 'as'
getMtags: no visible global function definition for 'is'
getOneHits: no visible global function definition for 'queryHits'
getOneHits: no visible global function definition for 'subjectHits'
getOneHits: no visible global function definition for 'metadata<-'
gwMatchPWM: no visible binding for global variable 'Hsapiens'
gwMatchPWM: no visible global function definition for 'is'
gwMatchPWM: no visible global function definition for '%dopar%'
gwMatchPWM: no visible global function definition for 'foreach'
gwMatchPWM: no visible binding for global variable 'i'
gwMatchPWM: no visible global function definition for 'matchPWM'
gwMatchPWM: no visible global function definition for
'PWMscoreStartingAt'
gwMatchPWM: no visible global function definition for 'subject'
gwMatchPWM: no visible global function definition for 'as'
rng2facHits: no visible global function definition for 'as'
rng2facHits: no visible global function definition for
'registerDoParallel'
rng2facHits: no visible global function definition for '%dopar%'
rng2facHits: no visible global function definition for 'foreach'
rng2facHits: no visible binding for global variable 'i'
runfimo: no visible global function definition for '%dopar%'
runfimo: no visible global function definition for 'foreach'
runfimo: no visible binding for global variable 'i'
setupGWPM: no visible global function definition for
'registerDoParallel'
Undefined global functions or variables:
%dopar% Hsapiens PWMscoreStartingAt as foreach i is matchPWM
metadata<- queryHits registerDoParallel subject subjectHits
Consider adding
importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: vtpnet-package.Rd:48-50: Dropping empty section \references
prepare_Rd: vtpnet-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: vtpnet-package.Rd:55-56: Dropping empty section \examples
* 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 ... NOTE
Error: package 'org.Hs.eg.db' required by 'Homo.sapiens' could not be found
Call sequence:
7: stop(gettextf("package %s required by %s could not be found",
sQuote(pkg), sQuote(pkgname)), call. = FALSE, domain = NA)
6: .getRequiredPackages2(pkgInfo, quietly = quietly)
5: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,
quietly = quietly)
4: .getRequiredPackages2(pkgInfo, quietly = quietly)
3: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,
quietly = quietly)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/vtpnet.Rcheck/00check.log'
for details.
vtpnet.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/vtpnet_0.23.0.tar.gz && rm -rf vtpnet.buildbin-libdir && mkdir vtpnet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=vtpnet.buildbin-libdir vtpnet_0.23.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL vtpnet_0.23.0.zip && rm vtpnet_0.23.0.tar.gz vtpnet_0.23.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 19.9M 100 19.9M 0 0 50.0M 0 --:--:-- --:--:-- --:--:-- 50.8M
install for i386
* installing *source* package 'vtpnet' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'vtpnet'
finding HTML links ... done
vtpnet-package html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'vtpnet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'vtpnet' as vtpnet_0.23.0.zip
* DONE (vtpnet)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'vtpnet' successfully unpacked and MD5 sums checked