Paul Shannon
| Snapshot Date: 2020-08-31 14:50:45 -0400 (Mon, 31 Aug 2020) |
| URL: https://git.bioconductor.org/packages/RefNet |
| Branch: RELEASE_3_11 |
| Last Commit: 716e288 |
| Last Changed Date: 2020-04-27 14:40:10 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-09-01 12:15:50 -0400 (Tue, 01 Sep 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE RefNet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1457/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Paul Shannon
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: RefNet |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RefNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RefNet_1.24.0.tar.gz |
| StartedAt: 2020-09-01 04:03:36 -0400 (Tue, 01 Sep 2020) |
| EndedAt: 2020-09-01 04:13:12 -0400 (Tue, 01 Sep 2020) |
| EllapsedTime: 575.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RefNet.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RefNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RefNet_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RefNet.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RefNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RefNet' version '1.24.0'
* 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 'RefNet' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'RefNet' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RefNet.Rcheck/00install.out' for details.
* 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 (user + system) or elapsed time > 5s
user system elapsed
RefNet-class 36.07 1.65 42.67
interactions 31.61 1.24 34.78
providerClasses 30.56 1.06 33.57
providers 26.87 1.01 29.90
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
providers 33.00 1.40 36.86
RefNet-class 30.34 1.28 33.82
interactions 30.52 0.98 33.53
providerClasses 30.28 1.06 33.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
RefNet RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R: Error while sourcing C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R : Error in IDMapper("9606") : url.exists(url) is not TRUE
Test files with failing tests
test_RefNet.R
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R
Error in BiocGenerics:::testPackage("RefNet") :
unit tests failed for package RefNet
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
RefNet RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R: Error while sourcing C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R : Error in IDMapper("9606") : url.exists(url) is not TRUE
Test files with failing tests
test_RefNet.R
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R
Error in BiocGenerics:::testPackage("RefNet") :
unit tests failed for package RefNet
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: 2 ERRORs, 1 WARNING
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/RefNet.Rcheck/00check.log'
for details.
RefNet.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/RefNet_1.24.0.tar.gz && rm -rf RefNet.buildbin-libdir && mkdir RefNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RefNet.buildbin-libdir RefNet_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL RefNet_1.24.0.zip && rm RefNet_1.24.0.tar.gz RefNet_1.24.0.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 92395 100 92395 0 0 1349k 0 --:--:-- --:--:-- --:--:-- 1503k
install for i386
* installing *source* package 'RefNet' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
** help
*** installing help indices
converting help for package 'RefNet'
finding HTML links ... done
RefNet-class html
detectDuplicateInteractions html
interactions html
pickBestFromDupGroup html
providerClasses html
providers html
pubmedAbstract html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
Warning: Package 'RefNet' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
Warning: Package 'RefNet' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'RefNet' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
Warning: Package 'RefNet' is deprecated and will be removed from Bioconductor
version 3.12
* MD5 sums
packaged installation of 'RefNet' as RefNet_1.24.0.zip
* DONE (RefNet)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'RefNet' successfully unpacked and MD5 sums checked
|
RefNet.Rcheck/tests_i386/runTests.Rout.fail
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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.
> require(RefNet) || stop("unable to load RefNet package")
Loading required package: RefNet
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
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 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
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: shiny
[1] TRUE
Warning messages:
1: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
2: Package 'RefNet' is deprecated and will be removed from Bioconductor
version 3.12
> BiocGenerics:::testPackage('RefNet')
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:AnnotationHub':
cache
The following object is masked from 'package:httr':
content
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2020-04-27
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
[1] RefNet ready.
checking for biomart access...
does 'http://www.ensembl.org' respond?
Error in IDMapper("9606") : url.exists(url) is not TRUE
RUNIT TEST PROTOCOL -- Tue Sep 01 04:11:48 2020
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
RefNet RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R: Error while sourcing C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R : Error in IDMapper("9606") : url.exists(url) is not TRUE
Test files with failing tests
test_RefNet.R
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R
Error in BiocGenerics:::testPackage("RefNet") :
unit tests failed for package RefNet
Execution halted
|
RefNet.Rcheck/tests_x64/runTests.Rout.fail
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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.
> require(RefNet) || stop("unable to load RefNet package")
Loading required package: RefNet
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
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 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
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: shiny
[1] TRUE
Warning messages:
1: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
2: Package 'RefNet' is deprecated and will be removed from Bioconductor
version 3.12
> BiocGenerics:::testPackage('RefNet')
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:AnnotationHub':
cache
The following object is masked from 'package:httr':
content
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2020-04-27
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
loading from cache
[1] RefNet ready.
checking for biomart access...
does 'http://www.ensembl.org' respond?
Error in IDMapper("9606") : url.exists(url) is not TRUE
RUNIT TEST PROTOCOL -- Tue Sep 01 04:13:01 2020
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
RefNet RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R: Error while sourcing C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R : Error in IDMapper("9606") : url.exists(url) is not TRUE
Test files with failing tests
test_RefNet.R
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RefNet/unitTests/test_RefNet.R
Error in BiocGenerics:::testPackage("RefNet") :
unit tests failed for package RefNet
Execution halted
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RefNet.Rcheck/examples_i386/RefNet-Ex.timings
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RefNet.Rcheck/examples_x64/RefNet-Ex.timings
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