Gregory Ryslik
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/QuartPAC |
| Branch: RELEASE_3_10 |
| Last Commit: c5fcfd7 |
| Last Changed Date: 2019-10-29 13:09:07 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:24:09 -0400 (Wed, 15 Apr 2020).
| Package 1351/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| QuartPAC 1.18.0 Gregory Ryslik
| malbec1 | Linux (Ubuntu 18.04.4 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: QuartPAC |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QuartPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings QuartPAC_1.18.0.tar.gz |
| StartedAt: 2020-04-15 05:49:21 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:54:06 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 285.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: QuartPAC.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QuartPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings QuartPAC_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/QuartPAC.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QuartPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QuartPAC' version '1.18.0'
* 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 'QuartPAC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
alignPositions: no visible global function definition for
'PhredQuality'
alignPositions: no visible global function definition for
'pairwiseAlignment'
constructCanonicalNumbering: no visible global function definition for
'pattern'
constructCanonicalNumbering: no visible global function definition for
'subject'
constructCanonicalNumbering: no visible global function definition for
'start'
getMutations : <anonymous>: no visible global function definition for
'read.table'
getRangeLocInfo: no visible global function definition for 'aggregate'
quartCluster: no visible global function definition for
'capture.output'
Undefined global functions or variables:
PhredQuality aggregate capture.output pairwiseAlignment pattern
read.table start subject
Consider adding
importFrom("stats", "aggregate", "start")
importFrom("utils", "capture.output", "read.table")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'QuartPAC-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QuartPAC-package
> ### Title: Identifying mutational clusters while incorporating protein
> ### quaternary structure.
> ### Aliases: QuartPAC-package QuartPAC
> ### Keywords: protein quaternary clustering
>
> ### ** Examples
>
>
> #read the mutational data
> mutation_files <- list(
+ system.file("extdata","HFE_Q30201_MutationOutput.txt", package = "QuartPAC"),
+ system.file("extdata","B2M_P61769_MutationOutput.txt", package = "QuartPAC")
+ )
> uniprots <- list("Q30201","P61769")
> mutation.data <- getMutations(mutation_files = mutation_files, uniprots = uniprots)
Warning in file(con, "r") :
InternetOpenUrl failed: 'An error occurred in the secure channel support'
Error in file(con, "r") : cannot open the connection
Calls: getMutations -> lapply -> FUN -> get.AASeq -> readLines -> file
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
QuartPAC-package 50.02 4.34 49.67
makeAlignedSuperStructure 24.62 4.73 24.41
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/QuartPAC.Rcheck/00check.log'
for details.
QuartPAC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/QuartPAC_1.18.0.tar.gz && rm -rf QuartPAC.buildbin-libdir && mkdir QuartPAC.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QuartPAC.buildbin-libdir QuartPAC_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL QuartPAC_1.18.0.zip && rm QuartPAC_1.18.0.tar.gz QuartPAC_1.18.0.zip
###
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install for i386
* installing *source* package 'QuartPAC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'QuartPAC'
finding HTML links ... done
QuartPAC-package html
getMutations html
makeAlignedSuperStructure html
quartCluster 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 'QuartPAC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QuartPAC' as QuartPAC_1.18.0.zip
* DONE (QuartPAC)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'QuartPAC' successfully unpacked and MD5 sums checked
|
QuartPAC.Rcheck/tests_i386/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("QuartPAC")
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:gdata':
combine
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:gdata':
first, first<-
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:gdata':
trim
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'igraph'
The following object is masked from 'package:Biostrings':
union
The following object is masked from 'package:IRanges':
union
The following object is masked from 'package:S4Vectors':
union
The following objects are masked from 'package:BiocGenerics':
normalize, path, union
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Attaching package: 'combinat'
The following object is masked from 'package:utils':
combn
Attaching package: 'data.table'
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
The following objects are masked from 'package:gdata':
first, last
Performing SpacePAC calculations
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.50
Performing iPAC Calculations
[1] "Running Remapped"
Performing GraphPAC Calculations
Calculating Remapped Clusters.
RUNIT TEST PROTOCOL -- Wed Apr 15 05:53:12 2020
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
QuartPAC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
40.68 4.43 41.79
|
QuartPAC.Rcheck/tests_x64/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("QuartPAC")
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:gdata':
combine
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:gdata':
first, first<-
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:gdata':
trim
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'igraph'
The following object is masked from 'package:Biostrings':
union
The following object is masked from 'package:IRanges':
union
The following object is masked from 'package:S4Vectors':
union
The following objects are masked from 'package:BiocGenerics':
normalize, path, union
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Attaching package: 'combinat'
The following object is masked from 'package:utils':
combn
Attaching package: 'data.table'
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
The following objects are masked from 'package:gdata':
first, last
Performing SpacePAC calculations
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.50
Performing iPAC Calculations
[1] "Running Remapped"
Performing GraphPAC Calculations
Calculating Remapped Clusters.
RUNIT TEST PROTOCOL -- Wed Apr 15 05:53:58 2020
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
QuartPAC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
45.56 5.31 45.53
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QuartPAC.Rcheck/examples_i386/QuartPAC-Ex.timings
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QuartPAC.Rcheck/examples_x64/QuartPAC-Ex.timings
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