| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:14:58 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 432/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CRISPRseek 1.39.0 (landing page) Lihua Julie Zhu
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: CRISPRseek |
| Version: 1.39.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CRISPRseek_1.39.0.tar.gz |
| StartedAt: 2023-02-06 22:32:05 -0000 (Mon, 06 Feb 2023) |
| EndedAt: 2023-02-06 22:51:46 -0000 (Mon, 06 Feb 2023) |
| EllapsedTime: 1180.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CRISPRseek.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CRISPRseek_1.39.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CRISPRseek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRISPRseek’ version ‘1.39.0’
* 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 for sufficient/correct file permissions ... 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 12.4Mb
* 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
* 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’
getOfftargetScore2: no visible binding for global variable ‘subPAM’
getOfftargetScoreBulge: no visible global function definition for
‘import’
predictRelativeFreqIndels : <anonymous>: no visible global function
definition for ‘predIndelFreq’
Undefined global functions or variables:
exons genes import predIndelFreq seqlevels<- subPAM
* 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:307-309: 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CRISPRseek-package 197.877 7.244 224.236
offTargetAnalysisWithoutBSgenome 52.888 0.293 56.108
offTargetAnalysis 14.436 0.107 16.159
compare2Sequences 9.874 0.034 11.466
filterOffTarget 4.584 0.072 5.466
searchHits2 4.145 0.320 5.130
annotateOffTargets 4.066 0.056 5.302
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
>>> Finding all hits in sequence chrX ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘CRISPRseek.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.
CRISPRseek.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CRISPRseek ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘CRISPRseek’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (CRISPRseek)
CRISPRseek.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
0.206 0.031 0.445
CRISPRseek.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.
> Sys.setenv(R_TESTS="")
> require("CRISPRseek") || stop("unable to load Package:CRISPRseek")
Loading required package: CRISPRseek
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, 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.max, which.min
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") ||
+ stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: rtracklayer
[1] TRUE
> require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db")
Loading required package: org.Hs.eg.db
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")'.
[1] TRUE
> require("TxDb.Hsapiens.UCSC.hg19.knownGene") ||
+ stop("unable to load TxDb.Hsapiens.UCSC.hg19.knownGene")
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
[1] TRUE
> require("BSgenome.Mmusculus.UCSC.mm10") ||
+ stop("unable to load Package: BSgenome.Mmusculus.UCSC.mm10")
Loading required package: BSgenome.Mmusculus.UCSC.mm10
[1] TRUE
> require("TxDb.Mmusculus.UCSC.mm10.knownGene") ||
+ stop("unable to load Package:TxDb.Mmusculus.UCSC.mm10.knownGene")
Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
[1] TRUE
> require("org.Mm.eg.db") ||
+ stop("unable to load Package:org.Mm.eg.db")
Loading required package: org.Mm.eg.db
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("CRISPRseek")
testing compare2Sequences
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Feb-06-2023/
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Feb-06-2023/
[1] "Scoring ..."
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 2
>>> Finding all hits in sequence rs362331T ...
>>> DONE searching
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Feb-06-2023/
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Feb-06-2023/
[1] "Scoring ..."
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 2
>>> Finding all hits in sequence rs362331T ...
>>> DONE searching
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Feb-06-2023/
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
Done. Please check output files in directory /home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Feb-06-2023/
[1] "Scoring ..."
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 2
>>> Finding all hits in sequence rs362331T ...
>>> DONE searching
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
search for gRNAs for input file1...
[1] "Scoring ..."
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 2
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
[1] "Scoring ..."
finish off-target search in sequence 2
>>> Finding all hits in sequence rs362331C ...
>>> DONE searching
finish off-target search in sequence 1
finish feature vector building
finish score calculation
[1] "Done!"
testing gRNAs provided and filter gRNAs with RE for offTargetAnalysis
Validating input ...
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Validating input ...
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Validating input ...
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Validating input ...
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
testing gRNAs provided without filtering gRNAs with RE for offTargetAnalysis
checking N in PAM...Testing for mouse with orgAnn...
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for mouse without orgAnn...
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for mouse without orgAnn...
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr13 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add paired information...
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Testing for findgRNAs = FALSE...
Validating input ...
>>> Finding all hits in sequence chr3 ...
>>> DONE searching
>>> Finding all hits in sequence chr4 ...
>>> DONE searching
>>> Finding all hits in sequence chr5 ...
>>> DONE searching
>>> Finding all hits in sequence chr6 ...
>>> DONE searching
>>> Finding all hits in sequence chr8 ...
>>> DONE searching
>>> Finding all hits in sequence chr11 ...
>>> DONE searching
>>> Finding all hits in sequence chr15 ...
>>> DONE searching
>>> Finding all hits in sequence chrX ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
Annotating, filtering and generating reports ...
Done annotating
Add RE information...
write gRNAs to bed file...
Scan for REsites in flanking region...
Done. Please check output files in directory
/home/biocbuild/bbs-3.17-bioc/meat/CRISPRseek.Rcheck/tests/testthat/
Validating input ...
Searching for gRNAs ...
>>> Finding all hits in sequence chr1 ...
Killed
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
| name | user | system | elapsed | |
| CRISPRseek-package | 197.877 | 7.244 | 224.236 | |
| annotateOffTargets | 4.066 | 0.056 | 5.302 | |
| buildFeatureVectorForScoring | 0.173 | 0.008 | 0.182 | |
| calculategRNAEfficiency | 0.022 | 0.000 | 0.051 | |
| compare2Sequences | 9.874 | 0.034 | 11.466 | |
| deepCpf1 | 0.08 | 0.00 | 0.08 | |
| filterOffTarget | 4.584 | 0.072 | 5.466 | |
| filtergRNAs | 0.908 | 0.000 | 1.100 | |
| findgRNAs | 0.358 | 0.004 | 0.422 | |
| getOfftargetScore | 0.109 | 0.000 | 0.110 | |
| isPatternUnique | 0.017 | 0.000 | 0.018 | |
| offTargetAnalysis | 14.436 | 0.107 | 16.159 | |
| offTargetAnalysisWithoutBSgenome | 52.888 | 0.293 | 56.108 | |
| predictRelativeFreqIndels | 0 | 0 | 0 | |
| searchHits | 0.196 | 0.004 | 0.224 | |
| searchHits2 | 4.145 | 0.320 | 5.130 | |
| translatePattern | 0.001 | 0.000 | 0.000 | |
| uniqueREs | 0.489 | 0.040 | 0.547 | |
| writeHits | 0 | 0 | 0 | |
| writeHits2 | 0.175 | 0.001 | 0.176 | |