Beth Signal
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/GeneStructureTools |
| Branch: RELEASE_3_7 |
| Last Commit: 291ec3a |
| Last Changed Date: 2018-04-30 10:35:49 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:45:25 -0400 (Wed, 17 Oct 2018).
| Package 579/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneStructureTools 1.0.0 Beth Signal
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GeneStructureTools |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GeneStructureTools_1.0.0.tar.gz |
| StartedAt: 2018-10-17 02:12:49 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:27:45 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 896.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GeneStructureTools_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GeneStructureTools.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneStructureTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneStructureTools' version '1.0.0'
* package encoding: UTF-8
* 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 'GeneStructureTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* 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 ... OK
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
leafcutterTranscriptChangeSummary 22.55 0.78 23.33
whippetTranscriptChangeSummary 10.81 0.03 11.94
alternativeIntronUsage 5.00 0.10 5.18
replaceJunction 4.61 0.00 6.70
** running examples for arch 'x64' ... ERROR
Running examples in 'GeneStructureTools-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readWhippetDataSet
> ### Title: Import whippet results files as a whippetDataSet
> ### Aliases: readWhippetDataSet
>
> ### ** Examples
>
> whippetFiles <- system.file("extdata","whippet/",
+ package = "GeneStructureTools")
> wds <- readWhippetDataSet(whippetFiles)
Taking input= as a system command ('gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/01_v_21.diff.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/A01.jnc.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/A21.jnc.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/B01.jnc.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/B21.jnc.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/A01.psi.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/A21.psi.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/B01.psi.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/B21.psi.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
0 [main] gzip 2568 c:\Rtools\bin\gzip.exe: *** fatal error - add_item ("\??\C:\cygwin", "/", ...) failed, errno 1
Stack trace:
Frame Function Args
End of stack trace
Warning in (if (.Platform$OS.type == "unix") system else shell)(paste0("(", :
'(gzip -dc C:/Users/biocbuild/bbs-3.7-bioc/R/library/GeneStructureTools/extdata/whippet/B21.psi.gz) > C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\RtmpEDQiFi\file15bc8ab977' execution failed with error code 256
Warning in data.table::fread(paste0(ungzip, files[f]), data.table = FALSE) :
File 'C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\RtmpEDQiFi\file15bc8ab977' has size 0. Returning a NULL data.frame.
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 15, 0
Calls: readWhippetDataSet ... readWhippetPSIfiles -> cbind -> cbind -> data.frame
Execution halted
* 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: 1 ERROR
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/GeneStructureTools.Rcheck/00check.log'
for details.
GeneStructureTools.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/GeneStructureTools_1.0.0.tar.gz && rm -rf GeneStructureTools.buildbin-libdir && mkdir GeneStructureTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneStructureTools.buildbin-libdir GeneStructureTools_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools_1.0.0.zip && rm GeneStructureTools_1.0.0.tar.gz GeneStructureTools_1.0.0.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 984k 100 984k 0 0 13.8M 0 --:--:-- --:--:-- --:--:-- 15.2M
install for i386
* installing *source* package 'GeneStructureTools' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GeneStructureTools'
finding HTML links ... done
DEXSeqIdsToGeneIds html
UTR2UTR53 html
addBroadTypes html
addIntronInTranscript html
addSets html
alternativeIntronUsage html
annotateGeneModel html
attrChangeAltSpliced html
coordinates-methods html
cumsumANDpad html
diffSplicingResults-methods html
exonsToTranscripts html
filterGtfOverlap html
filterWhippetEvents html
findDEXexonType html
findExonContainingTranscripts html
findIntronContainingTranscripts html
findJunctionPairs html
formatWhippetEvents html
getOrfs html
getUOrfs html
junctions-methods html
leafcutterTranscriptChangeSummary html
makeGeneModel html
maxLocation html
orfDiff html
orfSimilarity html
overlapTypes html
readCounts-methods html
readWhippetDIFFfiles html
readWhippetDataSet html
readWhippetJNCfiles html
readWhippetPSIfiles html
removeDuplicateTranscripts html
removeSameExon html
removeVersion html
reorderExonNumbers html
replaceJunction html
skipExonInTranscript html
summariseExonTypes html
transcriptChangeSummary html
whippetDataSet-class html
whippetTranscriptChangeSummary html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GeneStructureTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneStructureTools' as GeneStructureTools_1.0.0.zip
* DONE (GeneStructureTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GeneStructureTools' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
GeneStructureTools.Rcheck/examples_i386/GeneStructureTools-Ex.timings
|
GeneStructureTools.Rcheck/examples_x64/GeneStructureTools-Ex.timings
|