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This page was generated on 2023-06-06 11:00:29 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 443/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crisprDesign 1.3.1 (landing page) Jean-Philippe Fortin
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: crisprDesign |
| Version: 1.3.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings crisprDesign_1.3.1.tar.gz |
| StartedAt: 2023-06-05 20:22:15 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 20:35:20 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 785.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprDesign.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings crisprDesign_1.3.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/crisprDesign.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘crisprDesign/DESCRIPTION’ ... OK
* this is package ‘crisprDesign’ version ‘1.3.1’
* 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 17.099 0.088 17.223
addEditedAlleles 16.702 0.176 16.914
* 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.
crisprDesign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL crisprDesign ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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)
crisprDesign.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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.
> 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 ═══════════════════════════════════════════════════════════════
• empty test (69)
• long run time (8)
• no del for guideSetExample (1)
[ FAIL 0 | WARN 0 | SKIP 78 | PASS 1018 ]
>
> proc.time()
user system elapsed
240.838 4.208 246.104
crisprDesign.Rcheck/crisprDesign-Ex.timings
| name | user | system | elapsed | |
| GuideSet-class | 0.181 | 0.004 | 0.185 | |
| GuideSet2DataFrames | 2.335 | 0.031 | 2.371 | |
| PairedGuideSet-class | 0.529 | 0.023 | 0.554 | |
| TxDb2GRangesList | 0 | 0 | 0 | |
| addCompositeScores | 1.411 | 0.048 | 1.461 | |
| addDistanceToTss | 0.05 | 0.00 | 0.05 | |
| addEditedAlleles | 16.702 | 0.176 | 16.914 | |
| addExonTable | 0 | 0 | 0 | |
| addGeneAnnotation | 1.943 | 0.020 | 1.975 | |
| addIsoformAnnotation | 0.145 | 0.000 | 0.145 | |
| addNtcs | 0.437 | 0.004 | 0.442 | |
| addOffTargetScores | 0.321 | 0.004 | 0.325 | |
| addOnTargetScores | 0 | 0 | 0 | |
| addOpsBarcodes | 0.079 | 0.000 | 0.080 | |
| addPamScores | 0.590 | 0.000 | 0.592 | |
| addRepeats | 0.309 | 0.000 | 0.309 | |
| addRestrictionEnzymes | 0.986 | 0.016 | 1.004 | |
| addSNPAnnotation | 17.099 | 0.088 | 17.223 | |
| addSequenceFeatures | 0.603 | 0.004 | 0.608 | |
| addSpacerAlignments | 0.000 | 0.000 | 0.001 | |
| addTssAnnotation | 0.278 | 0.003 | 0.282 | |
| addTxTable | 0.000 | 0.000 | 0.001 | |
| completeSpacers | 0.472 | 0.012 | 0.487 | |
| convertToMinMaxGRanges | 0.082 | 0.000 | 0.083 | |
| convertToProtospacerGRanges | 0.300 | 0.012 | 0.313 | |
| designOpsLibrary | 0.149 | 0.000 | 0.149 | |
| findSpacerPairs | 2.869 | 0.023 | 2.901 | |
| findSpacers | 2.050 | 0.016 | 2.071 | |
| getBarcodeDistanceMatrix | 1.084 | 0.036 | 1.121 | |
| getConsensusIsoform | 0.09 | 0.00 | 0.09 | |
| getMrnaSequences | 0.392 | 0.004 | 0.398 | |
| getPreMrnaSequences | 0.344 | 0.012 | 0.356 | |
| getTssObjectFromTxObject | 0.077 | 0.004 | 0.081 | |
| getTxDb | 0 | 0 | 0 | |
| getTxInfoDataFrame | 0.869 | 0.048 | 0.918 | |
| preparePfamTable | 0.002 | 0.000 | 0.002 | |
| queryTss | 0.115 | 0.008 | 0.123 | |
| queryTxObject | 0.038 | 0.000 | 0.039 | |
| rankSpacers | 2.321 | 0.004 | 2.329 | |
| removeRepeats | 0.297 | 0.004 | 0.302 | |
| updateOpsLibrary | 0.232 | 0.004 | 0.236 | |
| validateOpsLibrary | 0.173 | 0.000 | 0.174 | |