| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:24 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the CRISPRseek package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CRISPRseek.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 416/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CRISPRseek 1.34.2 (landing page) Lihua Julie Zhu
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CRISPRseek |
| Version: 1.34.2 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRISPRseek.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CRISPRseek_1.34.2.tar.gz |
| StartedAt: 2022-04-12 17:58:20 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 18:13:47 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 927.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CRISPRseek.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRISPRseek.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CRISPRseek_1.34.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CRISPRseek/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CRISPRseek' version '1.34.2'
* 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 'CRISPRseek' can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.9Mb
sub-directories of 1Mb or more:
extdata 12.1Mb
* 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 ... NOTE
annotateOffTargets: no visible global function definition for 'exons'
annotateOffTargets: no visible global function definition for
'seqlevels<-'
annotateOffTargets: no visible global function definition for 'genes'
predictRelativeFreqIndels : <anonymous>: no visible global function
definition for 'predIndelFreq'
Undefined global functions or variables:
exons genes predIndelFreq seqlevels<-
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:64-66: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:67-69: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:86-88: Dropping empty section \details
prepare_Rd: buildFeatureVectorForScoring.Rd:89-91: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:99-101: Dropping empty section \references
prepare_Rd: compare2Sequences.Rd:263-265: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:266-268: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:151-153: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:154-156: Dropping empty section \note
prepare_Rd: filtergRNAs.Rd:48-50: Dropping empty section \details
prepare_Rd: filtergRNAs.Rd:51-53: Dropping empty section \note
prepare_Rd: filtergRNAs.Rd:70-72: Dropping empty section \references
prepare_Rd: findgRNAs.Rd:308-310: Dropping empty section \references
prepare_Rd: getOfftargetScore.Rd:79-81: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:23-25: Dropping empty section \details
prepare_Rd: isPatternUnique.Rd:26-28: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:37-39: Dropping empty section \references
prepare_Rd: isPatternUnique.Rd:40-42: Dropping empty section \seealso
prepare_Rd: offTargetAnalysis.Rd:438-440: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:441-443: Dropping empty section \note
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:440-442: Dropping empty section \details
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:443-445: Dropping empty section \note
prepare_Rd: searchHits.Rd:99-101: Dropping empty section \details
prepare_Rd: searchHits.Rd:102-104: Dropping empty section \note
prepare_Rd: searchHits.Rd:130-132: Dropping empty section \references
prepare_Rd: searchHits2.Rd:116-118: Dropping empty section \details
prepare_Rd: searchHits2.Rd:119-121: Dropping empty section \note
prepare_Rd: searchHits2.Rd:152-154: Dropping empty section \references
prepare_Rd: translatePattern.Rd:22-24: Dropping empty section \details
prepare_Rd: translatePattern.Rd:25-27: Dropping empty section \note
prepare_Rd: translatePattern.Rd:33-35: Dropping empty section \references
prepare_Rd: translatePattern.Rd:36-38: Dropping empty section \seealso
prepare_Rd: uniqueREs.Rd:46-48: Dropping empty section \details
prepare_Rd: uniqueREs.Rd:49-51: Dropping empty section \note
prepare_Rd: uniqueREs.Rd:61-63: Dropping empty section \references
prepare_Rd: uniqueREs.Rd:64-66: Dropping empty section \seealso
prepare_Rd: writeHits.Rd:89-91: Dropping empty section \details
prepare_Rd: writeHits.Rd:92-94: Dropping empty section \note
prepare_Rd: writeHits2.Rd:99-101: Dropping empty section \details
prepare_Rd: writeHits2.Rd:102-104: Dropping empty section \note
* 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 'CRISPRseek-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: offTargetAnalysis
> ### Title: Design target-specific guide RNAs for CRISPR-Cas9 system in one
> ### function
> ### Aliases: offTargetAnalysis
> ### Keywords: misc
>
> ### ** Examples
>
>
> library(CRISPRseek)
> library("BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: rtracklayer
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
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")'.
> library(org.Hs.eg.db)
> outputDir <- getwd()
> inputFilePath <- system.file("extdata", "inputseq.fa",
+ package = "CRISPRseek")
> REpatternFile <- system.file("extdata", "NEBenzymes.fa",
+ package = "CRISPRseek")
> results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE,
+ REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE,
+ annotatePaired = FALSE,
+ BSgenomeName = Hsapiens, chromToSearch = "chrX",
+ txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
+ orgAnn = org.Hs.egSYMBOL, max.mismatch = 1,
+ outputDir = outputDir, overwrite = TRUE)
Validating input ...
Warning in dir.create(outputDir) :
'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists
Searching for gRNAs ...
>>> Finding all hits in sequence chrX ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Warning in dir.create(outputDir) :
'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck/examples_i386/
>
> #### predict indels and their frequecies for target sites
>
> if (interactive())
+ {
+ results <- offTargetAnalysis(inputFilePath,findgRNAsWithREcutOnly = TRUE,
+ findPairedgRNAOnly = FALSE,
+ annotatePaired = FALSE,
+ BSgenomeName = Hsapiens, chromToSearch = "chrX",
+ txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
+ orgAnn = org.Hs.egSYMBOL, max.mismatch = 1,
+ outputDir = outputDir, overwrite = TRUE,
+ predIndelFreq=TRUE, predictIndelFreq.onTargetOnly= TRUE)
+
+ names(results$indelFreq)
+ head(results$indelFreq[[1]])
+ ### save the indel frequences to tab delimited files, one file for each target/offtarget site.
+ mapply(write.table, results$indelFreq, file=paste0(names(results$indelFreq), '.xls'), sep = "\t", row.names = FALSE)
+ }
> #### predict gRNA efficacy using CRISPRscan
> featureWeightMatrixFile <- system.file("extdata", "Morenos-Mateo.csv",
+ package = "CRISPRseek")
>
> results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE,
+ REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE,
+ annotatePaired = FALSE,
+ BSgenomeName = Hsapiens, chromToSearch = "chrX",
+ txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
+ orgAnn = org.Hs.egSYMBOL, max.mismatch = 1,
+ rule.set = "CRISPRscan",
+ baseBeforegRNA = 6, baseAfterPAM = 6,
+ featureWeightMatrixFile = featureWeightMatrixFile,
+ outputDir = outputDir, overwrite = TRUE)
Validating input ...
Warning in dir.create(outputDir) :
'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists
Searching for gRNAs ...
>>> Finding all hits in sequence chrX ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Warning in dir.create(outputDir) :
'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck/examples_i386/
>
> ######## PAM is on the 5 prime side, e.g., Cpf1
> results <- offTargetAnalysis(inputFilePath = system.file("extdata",
+ "cpf1-2.fa", package = "CRISPRseek"), findgRNAsWithREcutOnly = FALSE,
+ findPairedgRNAOnly = FALSE,
+ annotatePaired = FALSE,
+ BSgenomeName = Hsapiens,
+ chromToSearch = "chr8",
+ txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
+ orgAnn = org.Hs.egSYMBOL, max.mismatch = 4,
+ baseBeforegRNA = 8, baseAfterPAM = 26,
+ rule.set = "DeepCpf1",
+ overlap.gRNA.positions = c(19, 23),
+ useEfficacyFromInputSeq = FALSE,
+ outputDir = getwd(),
+ overwrite = TRUE, PAM.location = "5prime",PAM.size = 4,
+ PAM = "TTTN", PAM.pattern = "^TNNN", allowed.mismatch.PAM = 2,
+ subPAM.position = c(1,2))
Validating input ...
Warning in dir.create(outputDir) :
'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists
Searching for gRNAs ...
>>> Finding all hits in sequence chr8 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Warning in dir.create(outputDir) :
'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists
Error: Installation of Python not found, Python bindings not loaded.
Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment.
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CRISPRseek-package 204.71 7.12 211.88
offTargetAnalysis 61.77 1.96 66.51
offTargetAnalysisWithoutBSgenome 41.38 0.08 41.47
compare2Sequences 7.91 0.10 8.00
searchHits2 4.97 0.24 5.20
* 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck/00check.log'
for details.
CRISPRseek.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CRISPRseek_1.34.2.tar.gz && rm -rf CRISPRseek.buildbin-libdir && mkdir CRISPRseek.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CRISPRseek.buildbin-libdir CRISPRseek_1.34.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CRISPRseek_1.34.2.zip && rm CRISPRseek_1.34.2.tar.gz CRISPRseek_1.34.2.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
0 10.5M 0 44358 0 0 281k 0 0:00:38 --:--:-- 0:00:38 281k
18 10.5M 18 2045k 0 0 1777k 0 0:00:06 0:00:01 0:00:05 1777k
46 10.5M 46 4976k 0 0 2322k 0 0:00:04 0:00:02 0:00:02 2322k
81 10.5M 81 8823k 0 0 2813k 0 0:00:03 0:00:03 --:--:-- 2813k
100 10.5M 100 10.5M 0 0 3016k 0 0:00:03 0:00:03 --:--:-- 3016k
install for i386
* installing *source* package 'CRISPRseek' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CRISPRseek'
finding HTML links ... done
CRISPRseek-package html
annotateOffTargets html
buildFeatureVectorForScoring html
calculategRNAEfficiency html
compare2Sequences html
deepCpf1 html
filterOffTarget html
filtergRNAs html
findgRNAs html
getOfftargetScore html
isPatternUnique html
offTargetAnalysis html
offTargetAnalysisWithoutBSgenome html
predictRelativeFreqIndels html
searchHits html
searchHits2 html
translatePattern html
uniqueREs html
writeHits html
writeHits2 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 'CRISPRseek' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CRISPRseek' as CRISPRseek_1.34.2.zip
* DONE (CRISPRseek)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CRISPRseek' successfully unpacked and MD5 sums checked
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CRISPRseek.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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("CRISPRseek")
>
> proc.time()
user system elapsed
0.25 0.04 0.28
|
CRISPRseek.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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("CRISPRseek")
>
> proc.time()
user system elapsed
0.18 0.00 0.18
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CRISPRseek.Rcheck/examples_i386/CRISPRseek-Ex.timings
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CRISPRseek.Rcheck/examples_x64/CRISPRseek-Ex.timings
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