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This page was generated on 2024-03-27 11:35:46 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 456/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprDesign 1.4.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/crisprDesign
git_branch: RELEASE_3_18
git_last_commit: 47405b3
git_last_commit_date: 2023-10-24 11:43:12 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for crisprDesign on nebbiolo2


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: 1.4.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings crisprDesign_1.4.0.tar.gz
StartedAt: 2024-03-25 21:20:32 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-25 21:30:06 -0400 (Mon, 25 Mar 2024)
EllapsedTime: 573.6 seconds
RetCode: 0
Status:   OK  
CheckDir: crisprDesign.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings crisprDesign_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/crisprDesign.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘1.4.0’
* 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 ... 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 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
addSNPAnnotation 11.351  0.099  11.452
addEditedAlleles 10.529  0.248  10.777
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘intro.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/crisprDesign.Rcheck/00check.log’
for details.



Installation output

crisprDesign.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL crisprDesign
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> 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 1018 ]

══ 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 1018 ]
> 
> proc.time()
   user  system elapsed 
168.428   3.178 171.999 

Example timings

crisprDesign.Rcheck/crisprDesign-Ex.timings

nameusersystemelapsed
GuideSet-class0.2580.0050.262
GuideSet2DataFrames1.7030.1221.825
PairedGuideSet-class0.3440.0010.344
TxDb2GRangesList000
addCompositeScores0.9340.1521.085
addDistanceToTss0.0390.0000.039
addEditedAlleles10.529 0.24810.777
addExonTable0.0010.0000.000
addGeneAnnotation1.3890.0311.420
addIsoformAnnotation0.1730.0000.173
addNtcs0.3170.0000.318
addOffTargetScores0.2690.0000.270
addOnTargetScores0.0000.0000.001
addOpsBarcodes0.0360.0000.035
addPamScores0.4020.0000.402
addRepeats0.2130.0000.212
addRestrictionEnzymes0.7460.0310.779
addSNPAnnotation11.351 0.09911.452
addSequenceFeatures0.4360.0080.444
addSpacerAlignments000
addTssAnnotation0.1720.0000.172
addTxTable000
completeSpacers0.3110.0200.331
convertToMinMaxGRanges0.0580.0000.057
convertToProtospacerGRanges0.2130.0010.213
designOpsLibrary0.1130.0080.121
findSpacerPairs1.9440.0481.992
findSpacers1.4510.0391.491
getBarcodeDistanceMatrix2.8050.1472.953
getConsensusIsoform0.0590.0000.059
getMrnaSequences0.2710.0010.270
getPreMrnaSequences0.2100.0070.218
getTssObjectFromTxObject0.0470.0000.047
getTxDb000
getTxInfoDataFrame0.5460.0230.570
preparePfamTable0.0010.0000.002
queryTss0.0340.0000.034
queryTxObject0.0240.0030.028
rankSpacers1.5630.0161.579
removeRepeats0.2000.0070.208
updateOpsLibrary0.1670.0010.166
validateOpsLibrary0.160.000.16