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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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

Package 461/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprDesign 1.6.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/crisprDesign
git_branch: RELEASE_3_19
git_last_commit: 9c8b631
git_last_commit_date: 2024-04-30 11:43:47 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for crisprDesign on nebbiolo1

To the developers/maintainers of the crisprDesign package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crisprDesign.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: crisprDesign
Version: 1.6.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings crisprDesign_1.6.0.tar.gz
StartedAt: 2024-06-12 22:01:41 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 22:11:32 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 590.2 seconds
RetCode: 0
Status:   OK  
CheckDir: crisprDesign.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings crisprDesign_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/crisprDesign.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘crisprDesign/DESCRIPTION’ ... OK
* this is package ‘crisprDesign’ version ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘crisprDesign’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
addEditedAlleles 11.390  0.335  11.726
addSNPAnnotation 10.948  0.056  11.004
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/crisprDesign.Rcheck/00check.log’
for details.


Installation output

crisprDesign.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL crisprDesign
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘crisprDesign’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (crisprDesign)

Tests output

crisprDesign.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> library(testthat)
> library(crisprDesign)
Loading required package: crisprBase
> 
> test_check("crisprDesign")
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 7
# reads with at least one alignment: 6 (85.71%)
# reads that failed to align: 1 (14.29%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 7
# reads with at least one alignment: 6 (85.71%)
# reads that failed to align: 1 (14.29%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38 
[runCrisprBowtie] Searching for SpCas9 protospacers 
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[ FAIL 0 | WARN 0 | SKIP 78 | PASS 1090 ]

══ Skipped tests (78) ══════════════════════════════════════════════════════════
• empty test (69): 'test-GuideSet-class.R:214:1',
  'test-GuideSet-class.R:225:1', 'test-GuideSet-class.R:230:1',
  'test-addGeneAnnotation.R:17:1', 'test-addGeneAnnotation.R:116:1',
  'test-addGeneAnnotation.R:174:1', 'test-addNtcs.R:352:1',
  'test-addNtcs.R:398:1', 'test-addOffTargetScores.R:21:1',
  'test-addOnTargetScores.R:20:1', 'test-addOnTargetScores.R:67:1',
  'test-addOnTargetScores.R:87:1', 'test-addOnTargetScores.R:101:1',
  'test-addOnTargetScores.R:145:1', 'test-addOnTargetScores.R:157:1',
  'test-addOnTargetScores.R:190:1', 'test-addPamScores.R:30:1',
  'test-addRepeats.R:78:1', 'test-addRepeats.R:84:1', 'test-addRepeats.R:89:1',
  'test-addRestrictionEnzymes.R:89:1', 'test-addRestrictionEnzymes.R:180:1',
  'test-addRestrictionEnzymes.R:185:1', 'test-addRestrictionEnzymes.R:191:1',
  'test-addRestrictionEnzymes.R:198:1', 'test-addSpacerAlignments.R:63:1',
  'test-addSpacerAlignments.R:147:1', 'test-addSpacerAlignments.R:199:1',
  'test-addSpacerAlignments.R:266:1', 'test-addSpacerAlignments.R:349:1',
  'test-addSpacerAlignments.R:469:1', 'test-addSpacerAlignments.R:509:1',
  'test-addSpacerAlignments.R:546:1', 'test-addSpacerAlignments.R:572:1',
  'test-addSpacerAlignments.R:603:1', 'test-addSpacerAlignments.R:627:1',
  'test-addSpacerAlignments.R:650:1', 'test-addSpacerAlignments.R:669:1',
  'test-addSpacerAlignments.R:720:1', 'test-completeSpacers.R:27:1',
  'test-completeSpacers.R:32:1', 'test-completeSpacers.R:37:1',
  'test-completeSpacers.R:42:1', 'test-completeSpacers.R:47:1',
  'test-completeSpacers.R:52:1', 'test-completeSpacers.R:60:1',
  'test-completeSpacers.R:73:1', 'test-completeSpacers.R:78:1',
  'test-completeSpacers.R:83:1', 'test-completeSpacers.R:88:1',
  'test-completeSpacers.R:93:1', 'test-completeSpacers.R:113:1',
  'test-completeSpacers.R:118:1', 'test-completeSpacers.R:123:1',
  'test-completeSpacers.R:128:1', 'test-completeSpacers.R:133:1',
  'test-completeSpacers.R:139:1', 'test-completeSpacers.R:144:1',
  'test-completeSpacers.R:167:1', 'test-completeSpacers.R:172:1',
  'test-completeSpacers.R:177:1', 'test-completeSpacers.R:182:1',
  'test-completeSpacers.R:187:1', 'test-completeSpacers.R:193:1',
  'test-completeSpacers.R:198:1', 'test-completeSpacers.R:203:1',
  'test-completeSpacers.R:208:1', 'test-completeSpacers.R:213:1',
  'test-queryTxObject.R:152:1'
• long run time (8): 'test-TxDb2GRangesList.R:19:5',
  'test-TxDb2GRangesList.R:36:5', 'test-TxDb2GRangesList.R:56:5',
  'test-TxDb2GRangesList.R:77:5', 'test-addSNPAnnotation.R:33:5',
  'test-addSNPAnnotation.R:70:5', 'test-addSNPAnnotation.R:79:5',
  'test-addSNPAnnotation.R:124:5'
• no del for guideSetExample (1): 'test-addSNPAnnotation.R:148:5'

[ FAIL 0 | WARN 0 | SKIP 78 | PASS 1090 ]
> 
> proc.time()
   user  system elapsed 
168.028   5.652 174.258 

Example timings

crisprDesign.Rcheck/crisprDesign-Ex.timings

nameusersystemelapsed
GuideSet-class0.1350.0000.135
GuideSet2DataFrames2.3180.1872.506
PairedGuideSet-class0.3710.0390.411
TxDb2GRangesList000
addCompositeScores0.9300.0030.934
addDistanceToTss0.0420.0010.041
addEditedAlleles11.390 0.33511.726
addExonTable000
addGeneAnnotation1.3930.0571.449
addIsoformAnnotation0.1060.0000.107
addNtcs0.2990.0110.311
addOffTargetScores0.2570.0030.261
addOnTargetScores0.0010.0000.000
addOpsBarcodes0.0360.0010.036
addPamScores0.3730.0000.372
addRepeats0.2270.0080.235
addRestrictionEnzymes0.6640.0360.700
addSNPAnnotation10.948 0.05611.004
addSequenceFeatures0.3710.0030.376
addSpacerAlignments0.0010.0000.001
addTssAnnotation0.1620.0000.163
addTxTable0.0000.0000.001
completeSpacers0.3240.0310.357
convertToMinMaxGRanges0.0610.0040.065
convertToProtospacerGRanges0.2280.0040.232
designOpsLibrary0.1290.0000.129
findSpacerPairs1.9000.0951.997
findSpacers1.2330.0241.257
getBarcodeDistanceMatrix1.5500.0771.625
getConsensusIsoform0.070.000.07
getMrnaSequences0.2680.0190.288
getPreMrnaSequences0.2370.0160.253
getTssObjectFromTxObject0.0490.0040.052
getTxDb0.0000.0000.001
getTxInfoDataFrame0.6860.0670.754
preparePfamTable0.0020.0010.002
queryTss0.0150.0080.023
queryTxObject0.0320.0040.036
rankSpacers1.5740.0191.593
removeRepeats0.2230.0040.227
updateOpsLibrary0.1590.0010.159
validateOpsLibrary0.1460.0040.149