Gregory Ryslik
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/iPAC |
| Branch: RELEASE_3_8 |
| Last Commit: bebe766 |
| Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:16 -0400 (Sat, 13 Apr 2019).
| Package 789/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| iPAC 1.26.0 Gregory Ryslik
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: iPAC |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings iPAC_1.26.0.tar.gz |
| StartedAt: 2019-04-13 03:13:41 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:19:32 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 351.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: iPAC.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings iPAC_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/iPAC.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iPAC' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'iPAC' 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 ... NOTE
Packages in Depends field not imported from:
'Biostrings' 'gdata' 'multtest' 'scatterplot3d'
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
Plot.Protein.Linear: no visible global function definition for
'heat.colors'
Plot.Protein.Linear: no visible global function definition for 'gray'
Plot.Protein.Linear: no visible global function definition for
'topo.colors'
Plot.Protein.Linear: no visible global function definition for
'cm.colors'
Plot.Protein.Linear: no visible global function definition for 'par'
Plot.Protein.Linear: no visible global function definition for 'plot'
Plot.Protein.Linear: no visible global function definition for 'rect'
Plot.Protein.Linear: no visible global function definition for 'text'
SetTextContrastColor: no visible global function definition for
'col2rgb'
calcorder: no visible global function definition for 'dist'
calcorder: no visible global function definition for 'cmdscale'
difforder0: no visible global function definition for 'pbinom'
difforder0: no visible global function definition for 'dmultinom'
difforder1: no visible global function definition for 'dmultinom'
get.AlignedPositions: no visible global function definition for
'PhredQuality'
get.AlignedPositions: no visible global function definition for
'pairwiseAlignment'
get.AlignedPositions: no visible global function definition for 'start'
nmc: no visible global function definition for 'pbeta'
nmc: no visible global function definition for 'mt.rawp2adjp'
plotLinear: no visible global function definition for 'pdf'
plotLinear: no visible global function definition for 'scatterplot3d'
plotLinear: no visible global function definition for 'dev.off'
plotLinear: no visible global function definition for 'dev.copy2pdf'
plotMDS: no visible global function definition for 'pdf'
plotMDS: no visible global function definition for 'scatterplot3d'
plotMDS: no visible global function definition for 'dev.off'
plotMDS: no visible global function definition for 'dev.copy2pdf'
Undefined global functions or variables:
PhredQuality cm.colors cmdscale col2rgb dev.copy2pdf dev.off dist
dmultinom gray heat.colors mt.rawp2adjp pairwiseAlignment par pbeta
pbinom pdf plot rect scatterplot3d start text topo.colors
Consider adding
importFrom("grDevices", "cm.colors", "col2rgb", "dev.copy2pdf",
"dev.off", "gray", "heat.colors", "pdf", "topo.colors")
importFrom("graphics", "par", "plot", "rect", "text")
importFrom("stats", "cmdscale", "dist", "dmultinom", "pbeta", "pbinom",
"start")
to your NAMESPACE file.
* 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 ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ClusterFind 67.95 0.44 68.71
nmc 14.12 0.02 14.14
get.Positions 12.63 1.31 14.65
** running examples for arch 'x64' ... ERROR
Running examples in 'iPAC-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Plot.Protein.Linear
> ### Title: Plot.Protein.Linear
> ### Aliases: Plot.Protein.Linear
> ### Keywords: Order Mutations Amino Acids
>
> ### ** Examples
>
> #Extract the data from a CIF file and match it up with the canonical protein sequence.
> #Here we use the 3GFT structure from the PDB, which corresponds to the KRAS protein.
> CIF<-"https://files.rcsb.org/view/3GFT.cif"
> Fasta<-"https://www.uniprot.org/uniprot/P01116-2.fasta"
> KRAS.Positions<-get.Positions(CIF,Fasta, "A")
Warning in file(con, "r") :
cannot open URL 'https://www.uniprot.org/uniprot/P01116-2.fasta': HTTP status was '502 Proxy Error'
Error in file(con, "r") : cannot open the connection
Calls: get.Positions -> get.AASeq -> readLines -> file
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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/iPAC.Rcheck/00check.log'
for details.
iPAC.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/iPAC_1.26.0.tar.gz && rm -rf iPAC.buildbin-libdir && mkdir iPAC.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iPAC.buildbin-libdir iPAC_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL iPAC_1.26.0.zip && rm iPAC_1.26.0.tar.gz iPAC_1.26.0.zip
###
##############################################################################
##############################################################################
% 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 163k 100 163k 0 0 4743k 0 --:--:-- --:--:-- --:--:-- 5271k
install for i386
* installing *source* package 'iPAC' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'iPAC'
finding HTML links ... done
ClusterFind html
KRAS.Mutations html
PIK3CA.Mutations html
Plot.Protein.Linear html
get.AASeq html
get.AlignedPositions html
get.Positions html
get.Remapped.Order html
get.SingleLetterCode html
iPAC-package html
nmc html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'iPAC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iPAC' as iPAC_1.26.0.zip
* DONE (iPAC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'iPAC' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
iPAC.Rcheck/examples_i386/iPAC-Ex.timings
|
iPAC.Rcheck/examples_x64/iPAC-Ex.timings
|