Laurent Gatto
| Snapshot Date: 2019-04-06 17:01:31 -0400 (Sat, 06 Apr 2019) |
| URL: https://git.bioconductor.org/packages/pRoloc |
| Branch: master |
| Last Commit: 12e9698 |
| Last Changed Date: 2019-03-15 05:37:41 -0400 (Fri, 15 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-07 11:56:33 -0400 (Sun, 07 Apr 2019).
| Package 1234/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pRoloc 1.23.2 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: pRoloc |
| Version: 1.23.2 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pRoloc.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pRoloc_1.23.2.tar.gz |
| StartedAt: 2019-04-07 05:18:15 -0400 (Sun, 07 Apr 2019) |
| EndedAt: 2019-04-07 05:38:06 -0400 (Sun, 07 Apr 2019) |
| EllapsedTime: 1190.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: pRoloc.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pRoloc.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pRoloc_1.23.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pRoloc.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 'pRoloc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pRoloc' version '1.23.2'
* 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 'pRoloc' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-map.Rd:27: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-map.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-map.Rd:79: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-mcmc.Rd:24: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-mcmc.Rd:115: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-mcmc.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pRoloc.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 ... NOTE
Unexported objects imported by ':::' calls:
'MLInterfaces:::.macroF1' 'MLInterfaces:::.precision'
'MLInterfaces:::.recall' 'MLInterfaces:::es2df'
'MSnbase:::.sameNbCol' 'MSnbase:::getVariableName'
'MSnbase:::logging' 'MSnbase:::nologging' 'caret:::predict.plsda'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'pRoloc/R/annotation.R':
unlockBinding("params", .pRolocEnv)
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/pRoloc/libs/i386/pRoloc.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/pRoloc/libs/x64/pRoloc.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
perTurboClassification 10.76 0.00 10.80
nnetClassification 8.00 0.02 8.02
rfClassification 7.22 0.20 7.43
svmClassification 6.85 0.04 6.89
ClustDist-class 6.29 0.31 12.00
SpatProtVis-class 6.20 0.12 6.33
clustDist 4.11 0.26 14.81
ClustDistList-class 3.98 0.19 8.89
addGoAnnotations 3.77 0.27 9.31
AnnotationParams-class 0.78 0.11 33.59
makeGoSet 0.58 0.00 6.88
** running examples for arch 'x64' ... ERROR
Running examples in 'pRoloc-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AnnotationParams-class
> ### Title: Class '"AnnotationParams"'
> ### Aliases: class:AnnotationParams AnnotationParams AnnotationParams-class
> ### show,AnnotationParams-method AnnotationParams setAnnotationParams
> ### getAnnotationParams dunkley2006params andy2011params
> ### Keywords: classes
>
> ### ** Examples
>
> data(andy2011params)
> andy2011params
Object of class "AnnotationParams"
Using the 'ENSEMBL_MART_ENSEMBL' BioMart database
Using the 'hsapiens_gene_ensembl' dataset
Using 'uniprot_swissprot' as filter
Created on Wed Dec 9 11:27:10 2015
> data(dunkley2006params)
> dunkley2006params
Object of class "AnnotationParams"
Using the 'plants_mart' BioMart database
Using the 'athaliana_eg_gene' dataset
Using 'tair_locus' as filter
Created on Thu Apr 20 19:19:37 2017
>
> try(setAnnotationParams(inputs = c("nomatch1", "nomatch2")))
Error in setAnnotationParams(inputs = c("nomatch1", "nomatch2")) :
Couldn't find a unique species match for 'nomatch1'.
> setAnnotationParams(inputs = c("Homo sapiens",
+ "UniProtKB/Swiss-Prot ID"))
Using species Homo sapiens genes (GRCh38.p5)
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { :
argument is of length zero
Calls: setAnnotationParams -> getFilterList -> useMart -> listMarts
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
ER membrane 0 0 0
Golgi 0 0 0
Mitochondrion 0 0 0
PM 0 0 0
Plastid 0 0 0
Ribosome 0 0 0
TGN 13 0 0
unknown 0 428 0
vacuole 0 0 21
== testthat results ===========================================================
OK: 139 SKIPPED: 0 FAILED: 1
1. Error: AnnotationParams (@test_annotation.R#11)
Error: testthat unit tests failed
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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/pRoloc.Rcheck/00check.log'
for details.
pRoloc.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/pRoloc_1.23.2.tar.gz && rm -rf pRoloc.buildbin-libdir && mkdir pRoloc.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pRoloc.buildbin-libdir pRoloc_1.23.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL pRoloc_1.23.2.zip && rm pRoloc_1.23.2.tar.gz pRoloc_1.23.2.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 2530k 100 2530k 0 0 25.2M 0 --:--:-- --:--:-- --:--:-- 27.1M
install for i386
* installing *source* package 'pRoloc' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dmvtCpp.cpp -o dmvtCpp.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pRoloc.cpp -o pRoloc.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o pRoloc.dll tmp.def RcppExports.o dmvtCpp.o pRoloc.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/pRoloc.buildbin-libdir/00LOCK-pRoloc/00new/pRoloc/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'pRoloc'
finding HTML links ... done
AnnotationParams-class html
ClustDist-class html
ClustDistList-class html
GenRegRes-class html
finding level-2 HTML links ... done
MCMCParams html
MLearn-methods html
MartInstance-class html
QSep-class html
SpatProtVis-class html
addGoAnnotations html
addLegend html
addMarkers html
checkFeatureNamesOverlap html
checkFvarOverlap html
chi2-methods html
classWeights html
clustDist html
defunct html
empPvalues html
exprsToRatios-methods html
fDataToUnknown html
filterBinMSnSet html
filterMaxMarkers html
filterMinMarkers html
filterZeroCols html
getGOFromFeatures html
getMarkerClasses html
getMarkers html
getNormDist html
getPredictions html
getStockcol html
goIdToTerm html
highlightOnPlot html
knnClassification html
knnOptimisation html
knntlClassification html
knntlOptimisation html
ksvmClassification html
ksvmOptimisation html
lopims html
makeGoSet html
markerMSnSet html
markers html
mcmc-helpers html
minMarkers html
move2Ds html
mrkConsProfiles html
mrkHClust html
nbClassification html
nbOptimisation html
nndist-methods html
nnetClassification html
nnetOptimisation html
orderGoAnnotations html
orgQuants html
pRolocmarkers html
perTurboClassification html
perTurboOptimisation html
phenoDisco html
plot2D html
plot2Ds html
plotConsProfiles html
plotDist html
plotEllipse html
plsdaClassification html
plsdaOptimisation html
rfClassification html
rfOptimisation html
sampleMSnSet html
showGOEvidenceCodes html
subsetMarkers html
svmClassification html
svmOptimisation html
tagm-map html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-map.Rd:27: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-map.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-map.Rd:79: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
tagm-mcmc html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-mcmc.Rd:24: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-mcmc.Rd:115: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpigVsSF/R.INSTALL28c8206626bf/pRoloc/man/tagm-mcmc.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
testMSnSet html
testMarkers html
thetas html
undocumented html
zerosInBinMSnSet 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 'pRoloc' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dmvtCpp.cpp -o dmvtCpp.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pRoloc.cpp -o pRoloc.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o pRoloc.dll tmp.def RcppExports.o dmvtCpp.o pRoloc.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/pRoloc.buildbin-libdir/pRoloc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pRoloc' as pRoloc_1.23.2.zip
* DONE (pRoloc)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'pRoloc' successfully unpacked and MD5 sums checked
|
pRoloc.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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.
>
> # The setting of R_TESTS exists to work around an R bug. See
> # https://github.com/hadley/testthat/issues/144
> # We should remove it when the issue is resolved.
> Sys.setenv("R_TESTS" = "")
>
> library("testthat")
> library("pRoloc")
Loading required package: MSnbase
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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
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")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: ProtGenerics
This is MSnbase version 2.9.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XML
Attaching package: 'annotate'
The following object is masked from 'package:mzR':
nChrom
Loading required package: cluster
Loading required package: BiocParallel
This is pRoloc version 1.23.2
Visit https://lgatto.github.io/pRoloc/ to get started.
> library("pRolocdata")
This is pRolocdata version 1.21.0.
Use 'pRolocdata()' to list available data sets.
>
> test_check("pRoloc")
Object of class "SpatProtVis"
Data: dunkley2006
Visualisation methods: PCA, MDS, kpca
Done.
Connecting to Biomart...
Object of class "AnnotationParams"
Using the 'ENSEMBL_MART_ENSEMBL' BioMart database
Using the 'hsapiens_gene_ensembl' dataset
Using 'uniprotswissprot' as filter
Created on Sun Apr 07 05:28:14 2019
Connecting to Biomart...
GO Term Evidence Code
Experimental Evidence Codes
EXP: Inferred from Experiment
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
Computational Analysis Evidence Codes
ISS: Inferred from Sequence or Structural Similarity
ISO: Inferred from Sequence Orthology
ISA: Inferred from Sequence Alignment
ISM: Inferred from Sequence Model
IGC: Inferred from Genomic Context
IBA: Inferred from Biological aspect of Ancestor
IBD: Inferred from Biological aspect of Descendant
IKR: Inferred from Key Residues
IRD: Inferred from Rapid Divergence
RCA: inferred from Reviewed Computational Analysis
Author Statement Evidence Codes
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
Curator Statement Evidence Codes
IC: Inferred by Curator
ND: No biological Data available
Automatically-assigned Evidence Codes
IEA: Inferred from Electronic Annotation
Obsolete Evidence Codes
NR: Not Recorded
Connecting to Biomart...
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5
3 2 3 1 1
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5
5 2 1 1 1
organelleMarkers
ORG1 unknown
3 7
organelleMarkers
ORG1 unknown
2 8
# weights: 269
initial value 666.839513
iter 10 value 207.573433
iter 20 value 34.513121
iter 30 value 1.438035
iter 40 value 0.496168
iter 50 value 0.419018
iter 60 value 0.386372
iter 70 value 0.360129
iter 80 value 0.324298
iter 90 value 0.294123
iter 100 value 0.252996
final value 0.252996
stopped after 100 iterations
# weights: 269
initial value 666.839513
iter 10 value 207.573433
iter 20 value 34.513121
iter 30 value 1.438035
iter 40 value 0.496168
iter 50 value 0.419018
iter 60 value 0.386372
iter 70 value 0.360129
iter 80 value 0.324298
iter 90 value 0.294123
iter 100 value 0.252996
final value 0.252996
stopped after 100 iterations
Common markers: 0
Unique x markers: 49
Unique y markers: 34
Common unkowns: 11
Unique x unknowns: 40
Unique y unknowns: 66
my
mx ER lumen ER membrane Golgi Mitochondrion PM Plastid Ribosome
ER lumen 14 0 0 0 0 0 0
ER membrane 0 45 0 0 0 0 0
Golgi 0 0 28 0 0 0 0
Mitochondrion 0 0 0 55 0 0 0
PM 0 0 0 0 46 0 0
Plastid 0 0 0 0 0 20 0
Ribosome 0 0 0 0 0 0 19
TGN 0 0 0 0 0 0 0
unknown 0 0 0 0 0 0 0
vacuole 0 0 0 0 0 0 0
my
mx TGN unknown vacuole
ER lumen 0 0 0
ER membrane 0 0 0
Golgi 0 0 0
Mitochondrion 0 0 0
PM 0 0 0
Plastid 0 0 0
Ribosome 0 0 0
TGN 13 0 0
unknown 0 428 0
vacuole 0 0 21
== testthat results ===========================================================
OK: 147 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
113.90 3.54 299.10
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pRoloc.Rcheck/tests_x64/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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.
>
> # The setting of R_TESTS exists to work around an R bug. See
> # https://github.com/hadley/testthat/issues/144
> # We should remove it when the issue is resolved.
> Sys.setenv("R_TESTS" = "")
>
> library("testthat")
> library("pRoloc")
Loading required package: MSnbase
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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
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")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: ProtGenerics
This is MSnbase version 2.9.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XML
Attaching package: 'annotate'
The following object is masked from 'package:mzR':
nChrom
Loading required package: cluster
Loading required package: BiocParallel
This is pRoloc version 1.23.2
Visit https://lgatto.github.io/pRoloc/ to get started.
> library("pRolocdata")
This is pRolocdata version 1.21.0.
Use 'pRolocdata()' to list available data sets.
>
> test_check("pRoloc")
Object of class "SpatProtVis"
Data: dunkley2006
Visualisation methods: PCA, MDS, kpca
Done.
-- 1. Error: AnnotationParams (@test_annotation.R#11) -------------------------
invalid 'text' argument
1: setAnnotationParams(inputs = c("Homo sapiens", "UniProtKB/Swiss-Prot ID")) at testthat/test_annotation.R:11
2: getFilterList(m[spidx, "dataset"])
3: useMart(ds2[, "MartInterface"], dataset = ds, host = mi@host, path = mi@path)
4: useDataset(mart = mart, dataset = dataset, verbose = verbose)
5: bmAttrFilt("attributes", mart, verbose = verbose)
6: textConnection(attrfilt)
Connecting to Biomart...
GO Term Evidence Code
Experimental Evidence Codes
EXP: Inferred from Experiment
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
Computational Analysis Evidence Codes
ISS: Inferred from Sequence or Structural Similarity
ISO: Inferred from Sequence Orthology
ISA: Inferred from Sequence Alignment
ISM: Inferred from Sequence Model
IGC: Inferred from Genomic Context
IBA: Inferred from Biological aspect of Ancestor
IBD: Inferred from Biological aspect of Descendant
IKR: Inferred from Key Residues
IRD: Inferred from Rapid Divergence
RCA: inferred from Reviewed Computational Analysis
Author Statement Evidence Codes
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
Curator Statement Evidence Codes
IC: Inferred by Curator
ND: No biological Data available
Automatically-assigned Evidence Codes
IEA: Inferred from Electronic Annotation
Obsolete Evidence Codes
NR: Not Recorded
Connecting to Biomart...
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5
3 2 3 1 1
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5
5 2 1 1 1
organelleMarkers
ORG1 unknown
3 7
organelleMarkers
ORG1 unknown
2 8
# weights: 269
initial value 666.839513
iter 10 value 207.573433
iter 20 value 34.513121
iter 30 value 1.438035
iter 40 value 0.496168
iter 50 value 0.419018
iter 60 value 0.386372
iter 70 value 0.360129
iter 80 value 0.324298
iter 90 value 0.294123
iter 100 value 0.252996
final value 0.252996
stopped after 100 iterations
# weights: 269
initial value 666.839513
iter 10 value 207.573433
iter 20 value 34.513121
iter 30 value 1.438035
iter 40 value 0.496168
iter 50 value 0.419018
iter 60 value 0.386372
iter 70 value 0.360129
iter 80 value 0.324298
iter 90 value 0.294123
iter 100 value 0.252996
final value 0.252996
stopped after 100 iterations
Common markers: 0
Unique x markers: 49
Unique y markers: 34
Common unkowns: 11
Unique x unknowns: 40
Unique y unknowns: 66
my
mx ER lumen ER membrane Golgi Mitochondrion PM Plastid Ribosome
ER lumen 14 0 0 0 0 0 0
ER membrane 0 45 0 0 0 0 0
Golgi 0 0 28 0 0 0 0
Mitochondrion 0 0 0 55 0 0 0
PM 0 0 0 0 46 0 0
Plastid 0 0 0 0 0 20 0
Ribosome 0 0 0 0 0 0 19
TGN 0 0 0 0 0 0 0
unknown 0 0 0 0 0 0 0
vacuole 0 0 0 0 0 0 0
my
mx TGN unknown vacuole
ER lumen 0 0 0
ER membrane 0 0 0
Golgi 0 0 0
Mitochondrion 0 0 0
PM 0 0 0
Plastid 0 0 0
Ribosome 0 0 0
TGN 13 0 0
unknown 0 428 0
vacuole 0 0 21
== testthat results ===========================================================
OK: 139 SKIPPED: 0 FAILED: 1
1. Error: AnnotationParams (@test_annotation.R#11)
Error: testthat unit tests failed
Execution halted
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pRoloc.Rcheck/examples_i386/pRoloc-Ex.timings
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pRoloc.Rcheck/examples_x64/pRoloc-Ex.timings
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