Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:24 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for CRISPRseek on tokay2


To the developers/maintainers of the CRISPRseek package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]: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.

raw results

Package 416/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.34.2  (landing page)
Lihua Julie Zhu
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/CRISPRseek
git_branch: RELEASE_3_14
git_last_commit: c5ca587
git_last_commit_date: 2022-04-11 12:50:34 -0400 (Mon, 11 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.


Installation output

CRISPRseek.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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

Tests output

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 

Example timings

CRISPRseek.Rcheck/examples_i386/CRISPRseek-Ex.timings

nameusersystemelapsed
CRISPRseek-package214.44 8.28222.72
annotateOffTargets3.890.204.09
buildFeatureVectorForScoring0.080.000.08
calculategRNAEfficiency0.020.000.02
compare2Sequences7.840.107.93
deepCpf1000
filterOffTarget4.190.064.25
filtergRNAs0.610.000.61
findgRNAs0.270.000.26
getOfftargetScore0.110.000.11
isPatternUnique0.010.000.02

CRISPRseek.Rcheck/examples_x64/CRISPRseek-Ex.timings

nameusersystemelapsed
CRISPRseek-package204.71 7.12211.88
annotateOffTargets3.110.093.20
buildFeatureVectorForScoring0.080.000.08
calculategRNAEfficiency0.010.000.01
compare2Sequences7.910.108.00
deepCpf1000
filterOffTarget3.410.113.52
filtergRNAs0.620.000.62
findgRNAs0.270.000.29
getOfftargetScore0.080.000.07
isPatternUnique0.010.000.02
offTargetAnalysis61.77 1.9666.51
offTargetAnalysisWithoutBSgenome41.38 0.0841.47
predictRelativeFreqIndels0.040.000.05
searchHits0.290.000.29
searchHits24.970.245.20
translatePattern0.020.000.01
uniqueREs0.330.010.34
writeHits0.020.000.02
writeHits20.190.000.19