Lihua Julie Zhu
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/GUIDEseq |
| git_branch: RELEASE_3_17 |
| git_last_commit: 3970f96 |
| git_last_commit_date: 2023-04-25 10:42:14 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 900/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GUIDEseq 1.30.0 (landing page) Lihua Julie Zhu
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the GUIDEseq package: - 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. |
| Package: GUIDEseq |
| Version: 1.30.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GUIDEseq_1.30.0.tar.gz |
| StartedAt: 2023-10-17 23:53:14 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-18 00:05:51 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 757.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GUIDEseq.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GUIDEseq_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GUIDEseq.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GUIDEseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GUIDEseq’ version ‘1.30.0’
* 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 ‘GUIDEseq’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.5Mb
sub-directories of 1Mb or more:
extdata 12.0Mb
* 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 ... NOTE
':::' call which should be '::': ‘CRISPRseek:::translatePattern’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotTracks: warning in scale_x_continuous(label =
xaxis.lab.pos$chromosome, breaks = xaxis.lab.pos$chr.center): partial
argument match of 'label' to 'labels'
.maskSubSeq: no visible global function definition for ‘.getMatchedInd’
.nucleotideSubstitutionMatrix: no visible binding for global variable
‘IUPAC_CODE_MAP’
.nucleotideSubstitutionMatrix: no visible binding for global variable
‘DNA_BASES’
GUIDEseqAnalysis: no visible binding for global variable ‘offTarget’
GUIDEseqAnalysis: no visible binding for global variable ‘peak_score’
GUIDEseqAnalysis: no visible binding for global variable
‘predicted_cleavage_score’
GUIDEseqAnalysis: no visible binding for global variable ‘gRNA.name’
GUIDEseqAnalysis: no visible binding for global variable ‘gRNAPlusPAM’
GUIDEseqAnalysis: no visible binding for global variable
‘offTarget_sequence’
GUIDEseqAnalysis: no visible binding for global variable
‘guideAlignment2OffTarget’
GUIDEseqAnalysis: no visible binding for global variable
‘offTargetStrand’
GUIDEseqAnalysis: no visible binding for global variable
‘mismatch.distance2PAM’
GUIDEseqAnalysis: no visible binding for global variable
‘n.guide.mismatch’
GUIDEseqAnalysis: no visible binding for global variable
‘offTarget_Start’
GUIDEseqAnalysis: no visible binding for global variable
‘offTarget_End’
GUIDEseqAnalysis: no visible binding for global variable ‘chromosome’
GUIDEseqAnalysis: no visible binding for global variable
‘gRNA.insertion’
GUIDEseqAnalysis: no visible binding for global variable
‘gRNA.deletion’
GUIDEseqAnalysis: no visible binding for global variable
‘pos.insertion’
GUIDEseqAnalysis: no visible binding for global variable ‘pos.deletion’
GUIDEseqAnalysis: no visible binding for global variable ‘n.insertion’
GUIDEseqAnalysis: no visible binding for global variable ‘n.deletion’
GUIDEseqAnalysis: no visible binding for global variable ‘n.RNA.bulge’
GUIDEseqAnalysis: no visible binding for global variable ‘n.DNA.bulge’
GUIDEseqAnalysis: no visible binding for global variable ‘feature’
GUIDEseqAnalysis: no visible binding for global variable
‘n.distinct.UMIs’
annotateOffTargets: no visible binding for global variable
‘offTarget_Start’
getAlnWithBulge : <anonymous>: no visible binding for global variable
‘pa.f1’
getAlnWithBulge : <anonymous>: no visible binding for global variable
‘pa.r2’
getPeaks: no visible binding for global variable ‘adjusted.p.value’
getPeaks: no visible binding for global variable ‘SNratio’
getUniqueCleavageEvents: no visible binding for global variable
‘width.first’
getUniqueCleavageEvents: no visible binding for global variable
‘width.last’
getUniqueCleavageEvents: no visible binding for global variable
‘qwidth.last’
getUniqueCleavageEvents: no visible binding for global variable
‘strand.last’
getUniqueCleavageEvents: no visible binding for global variable
‘qwidth.first’
getUniqueCleavageEvents: no visible binding for global variable
‘strand.first’
getUniqueCleavageEvents: no visible binding for global variable
‘readName’
getUniqueCleavageEvents: no visible binding for global variable
‘seqnames.last’
getUniqueCleavageEvents: no visible binding for global variable
‘seqnames.first’
getUniqueCleavageEvents: no visible binding for global variable
‘start.last’
getUniqueCleavageEvents: no visible binding for global variable
‘end.first’
getUniqueCleavageEvents: no visible binding for global variable ‘UMI’
getUniqueCleavageEvents: no visible binding for global variable
‘start.first’
getUniqueCleavageEvents: no visible binding for global variable
‘end.last’
offTargetAnalysisOfPeakRegions: no visible binding for global variable
‘thePeak’
offTargetAnalysisOfPeakRegions: no visible binding for global variable
‘gRNAPlusPAM’
offTargetAnalysisOfPeakRegions: no visible binding for global variable
‘offTarget’
plotAlignedOfftargets: no visible binding for global variable
‘total.mismatch.bulge’
plotAlignedOfftargets: no visible binding for global variable ‘RIR’
plotAlignedOfftargets: no visible binding for global variable
‘guideAlignment2OffTarget’
plotAlignedOfftargets: no visible binding for global variable
‘DNA.bulge’
plotAlignedOfftargets: no visible binding for global variable ‘y’
plotAlignedOfftargets: no visible binding for global variable ‘h’
plotAlignedOfftargets: no visible binding for global variable ‘IR’
plotHeatmapOfftargets: no visible binding for global variable
‘total.mismatch.bulge’
plotHeatmapOfftargets: no visible binding for global variable
‘Offtargets’
plotHeatmapOfftargets: no visible binding for global variable ‘IR’
plotHeatmapOfftargets: no visible binding for global variable
‘Ontarget’
plotHeatmapOfftargets: no visible binding for global variable ‘IR.max’
plotHeatmapOfftargets: no visible binding for global variable ‘Samples’
plotHeatmapOfftargets: no visible global function definition for
‘guides’
plotHeatmapOfftargets: no visible global function definition for
‘guide_legend’
plotHeatmapOfftargets: no visible global function definition for ‘unit’
plotTracks: no visible binding for global variable
‘total.mismatch.bulge’
plotTracks: no visible binding for global variable ‘n.PAM.mismatch’
plotTracks: no visible binding for global variable ‘offTargetStrand’
plotTracks: no visible binding for global variable ‘offTarget_Start’
plotTracks: no visible binding for global variable ‘offTarget_End’
plotTracks: no visible binding for global variable ‘n.distinct.UMIs’
plotTracks: no visible binding for global variable
‘predicted_cleavage_score’
plotTracks: no visible global function definition for ‘geom_smooth’
plotTracks: no visible binding for global variable ‘chromosome’
plotTracks: no visible binding for global variable ‘chr.max’
plotTracks: no visible binding for global variable ‘chr.offset’
plotTracks: no visible binding for global variable ‘.’
plotTracks: no visible binding for global variable
‘cum.cleavage.position’
Undefined global functions or variables:
. .getMatchedInd DNA.bulge DNA_BASES IR IR.max IUPAC_CODE_MAP
Offtargets Ontarget RIR SNratio Samples UMI adjusted.p.value chr.max
chr.offset chromosome cum.cleavage.position end.first end.last
feature gRNA.deletion gRNA.insertion gRNA.name gRNAPlusPAM
geom_smooth guideAlignment2OffTarget guide_legend guides h
mismatch.distance2PAM n.DNA.bulge n.PAM.mismatch n.RNA.bulge
n.deletion n.distinct.UMIs n.guide.mismatch n.insertion offTarget
offTargetStrand offTarget_End offTarget_Start offTarget_sequence
pa.f1 pa.r2 peak_score pos.deletion pos.insertion
predicted_cleavage_score qwidth.first qwidth.last readName
seqnames.first seqnames.last start.first start.last strand.first
strand.last thePeak total.mismatch.bulge unit width.first width.last
y
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:35-37: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:63-65: Dropping empty section \references
prepare_Rd: createBarcodeFasta.Rd:56-58: Dropping empty section \references
prepare_Rd: getUsedBarcodes.Rd:53-55: Dropping empty section \references
checkRd: (-1) mergePlusMinusPeaks.Rd:72: Escaped LaTeX specials: \_
* 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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PEtagAnalysis 14.863 0.774 22.174
annotateOffTargets 7.217 0.365 11.673
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GUIDEseq.Rcheck/00check.log’
for details.
GUIDEseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GUIDEseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘GUIDEseq’ ... ** using staged installation ** R ** data ** 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 (GUIDEseq)
GUIDEseq.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(GUIDEseq)
Loading required package: GenomicRanges
Loading required package: stats4
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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
> library(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")'.
>
> test_check("GUIDEseq")
Loading required package: GenomicFeatures
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
GUIDEseqAnalysis without bulge.
Remove duplicate reads ...
Peak calling ...
computing coverage for plus strand ...
computing coverage for minus strand ...
call peaks ...
finding local max for chromosome: chr13
combine plus and minus peaks ...
keep peaks not in merged.gr but present in both peaks1 and peaks2
Find unmerged peaks with very high reads one-library protocol
offtarget analysis ...
search for gRNAs for input file1...
[1] "Scoring ..."
>>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629400:27629404 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:30964712:30964730 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:67161908:67161923 ...
>>> DONE searching
>>> Finding all hits in sequence chr13-:29087136:29087137 ...
>>> DONE searching
>>> Finding all hits in sequence chr13-:115084360:115084375 ...
>>> 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!"
Extract PAM sequence and n.PAM.mismatch.
Done with offtarget search!
Add gene and exon information to offTargets ....
Order offtargets.
Add sequence depth information.
Get the number of unique UMIs for each offtarget.
Save offtargets.
Please check output file in directory GUIDEseqTestResults
Remove duplicate reads ...
offtarget analysis ...
Done with offtarget search!
Add gene and exon information to offTargets ....
Order offtargets.
Add sequence depth information.
Get the number of unique UMIs for each offtarget.
Save offtargets.
Please check output file in directory GUIDEseqTestResults
GUIDEseqAnalysis with offtargets containing no bulge and with bulge.
Remove duplicate reads ...
Peak calling ...
computing coverage for plus strand ...
computing coverage for minus strand ...
call peaks ...
finding local max for chromosome: chr13
combine plus and minus peaks ...
keep peaks not in merged.gr but present in both peaks1 and peaks2
Find unmerged peaks with very high reads one-library protocol
offtarget analysis ...
search for gRNAs for input file1...
[1] "Scoring ..."
>>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629400:27629404 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:30964712:30964730 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:67161908:67161923 ...
>>> DONE searching
>>> Finding all hits in sequence chr13-:29087136:29087137 ...
>>> DONE searching
>>> Finding all hits in sequence chr13-:115084360:115084375 ...
>>> 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!"
Extract PAM sequence and n.PAM.mismatch.
Finding offtargets with bulges ...Done with offtarget search!
Add gene and exon information to offTargets ....
Order offtargets.
Add sequence depth information.
Get the number of unique UMIs for each offtarget.
Save offtargets.
Please check output file in directory GUIDEseqTestResults2
Remove duplicate reads ...
offtarget analysis ...
Finding offtargets with bulges ...Done with offtarget search!
Add gene and exon information to offTargets ....
Order offtargets.
Add sequence depth information.
Get the number of unique UMIs for each offtarget.
Save offtargets.
Please check output file in directory GUIDEseqTestResults2
GUIDEseqAnalysis with bulge containing offtargets where no offtargets contain no bulge.
Remove duplicate reads ...
Peak calling ...
computing coverage for plus strand ...
computing coverage for minus strand ...
call peaks ...
finding local max for chromosome: chr13
combine plus and minus peaks ...
keep peaks not in merged.gr but present in both peaks1 and peaks2
Find unmerged peaks with very high reads one-library protocol
offtarget analysis ...
search for gRNAs for input file1...
[1] "Scoring ..."
>>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629400:27629404 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:30964712:30964730 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:66687218:66687225 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:67161908:67161923 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:98226906:98226924 ...
>>> DONE searching
>>> Finding all hits in sequence chr13-:29087136:29087137 ...
>>> DONE searching
>>> Finding all hits in sequence chr13-:97395652:97395666 ...
>>> DONE searching
>>> Finding all hits in sequence chr13-:115084360:115084375 ...
>>> DONE searching
finish off-target search in sequence 2
finish off-target search in sequence 1
Remove duplicate reads ...
Peak calling ...
computing coverage for plus strand ...
computing coverage for minus strand ...
call peaks ...
finding local max for chromosome: chr13
combine plus and minus peaks ...
keep peaks not in merged.gr but present in both peaks1 and peaks2
Find unmerged peaks with very high reads one-library protocol
offtarget analysis ...
search for gRNAs for input file1...
[1] "Scoring ..."
>>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629399:27629417 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:39262920:39262939:chr13-:39262918:39262918 ...
>>> 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!"
Extract PAM sequence and n.PAM.mismatch.
Done with offtarget search!
Add gene and exon information to offTargets ....
Order offtargets.
Add sequence depth information.
Get the number of unique UMIs for each offtarget.
Save offtargets.
Please check output file in directory PEtagTestResults
search for gRNAs for input file1...
[1] "Scoring ..."
>>> Finding all hits in sequence chr13+:27629413:27629420:chr13-:27629400:27629404 ...
>>> DONE searching
>>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ...
>>> 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!"
bulge on gRNA and offtarget on the minus strand worksStart testing offtarget on the minus strand ...test sequence not long enough for allowing large stretch of bulge[ FAIL 0 | WARN 6 | SKIP 0 | PASS 259 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 259 ]
>
> proc.time()
user system elapsed
133.824 3.719 208.838
GUIDEseq.Rcheck/GUIDEseq-Ex.timings
| name | user | system | elapsed | |
| GUIDEseq-package | 0.001 | 0.001 | 0.002 | |
| GUIDEseqAnalysis | 0.001 | 0.000 | 0.005 | |
| PEtagAnalysis | 14.863 | 0.774 | 22.174 | |
| annotateOffTargets | 7.217 | 0.365 | 11.673 | |
| buildFeatureVectorForScoringBulge | 0.001 | 0.000 | 0.001 | |
| combineOfftargets | 0.093 | 0.024 | 0.183 | |
| createBarcodeFasta | 0.021 | 0.002 | 0.032 | |
| getPeaks | 0 | 0 | 0 | |
| getUniqueCleavageEvents | 0.000 | 0.001 | 0.002 | |
| getUsedBarcodes | 0.044 | 0.004 | 0.074 | |
| mergePlusMinusPeaks | 0.001 | 0.000 | 0.001 | |
| offTargetAnalysisOfPeakRegions | 0.001 | 0.000 | 0.003 | |
| offTargetAnalysisWithBulge | 0.001 | 0.001 | 0.001 | |
| peaks.gr | 0.031 | 0.007 | 0.058 | |
| plotAlignedOfftargets | 0.787 | 0.028 | 1.242 | |
| plotHeatmapOfftargets | 0.006 | 0.000 | 0.011 | |
| plotTracks | 0.016 | 0.001 | 0.026 | |
| uniqueCleavageEvents | 0.055 | 0.007 | 0.092 | |