##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GUIDEseq_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GUIDEseq.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GUIDEseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GUIDEseq’ version ‘1.37.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/GUIDEseq.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 12.6Mb
  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 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
Unexported objects imported by ':::' calls:
  'CRISPRseek:::getOfftargetScore2' 'CRISPRseek:::getSeqFromBed'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
.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 ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
PEtagAnalysis      20.703  0.675  21.447
annotateOffTargets  7.628  0.123   7.800
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GUIDEseq.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GUIDEseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘GUIDEseq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (GUIDEseq)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(GUIDEseq)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
Warning: program compiled against libxml 212 using older 211
> 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: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:BiocIO':

    FileForFormat

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 in sequence chr13+:27629413:27629420:chr13-:27629400:27629404!
  >>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ...
  >>> DONE searching in sequence chr13+:39262927:39262939:chr13-:39262918:39262920!
  >>> Finding all hits in sequence chr13+:30964712:30964730 ...
  >>> DONE searching in sequence chr13+:30964712:30964730!
  >>> Finding all hits in sequence chr13+:67161908:67161923 ...
  >>> DONE searching in sequence chr13+:67161908:67161923!
  >>> Finding all hits in sequence chr13-:29087136:29087137 ...
  >>> DONE searching in sequence chr13-:29087136:29087137!
  >>> Finding all hits in sequence chr13-:115084360:115084375 ...
  >>> DONE searching in sequence chr13-:115084360:115084375!
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 in sequence chr13+:27629413:27629420:chr13-:27629400:27629404!
  >>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ...
  >>> DONE searching in sequence chr13+:39262927:39262939:chr13-:39262918:39262920!
  >>> Finding all hits in sequence chr13+:30964712:30964730 ...
  >>> DONE searching in sequence chr13+:30964712:30964730!
  >>> Finding all hits in sequence chr13+:67161908:67161923 ...
  >>> DONE searching in sequence chr13+:67161908:67161923!
  >>> Finding all hits in sequence chr13-:29087136:29087137 ...
  >>> DONE searching in sequence chr13-:29087136:29087137!
  >>> Finding all hits in sequence chr13-:115084360:115084375 ...
  >>> DONE searching in sequence chr13-:115084360:115084375!
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 in sequence chr13+:27629413:27629420:chr13-:27629400:27629404!
  >>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ...
  >>> DONE searching in sequence chr13+:39262927:39262939:chr13-:39262918:39262920!
  >>> Finding all hits in sequence chr13+:30964712:30964730 ...
  >>> DONE searching in sequence chr13+:30964712:30964730!
  >>> Finding all hits in sequence chr13+:66687218:66687225 ...
  >>> DONE searching in sequence chr13+:66687218:66687225!
  >>> Finding all hits in sequence chr13+:67161908:67161923 ...
  >>> DONE searching in sequence chr13+:67161908:67161923!
  >>> Finding all hits in sequence chr13+:98226906:98226924 ...
  >>> DONE searching in sequence chr13+:98226906:98226924!
  >>> Finding all hits in sequence chr13-:29087136:29087137 ...
  >>> DONE searching in sequence chr13-:29087136:29087137!
  >>> Finding all hits in sequence chr13-:97395652:97395666 ...
  >>> DONE searching in sequence chr13-:97395652:97395666!
  >>> Finding all hits in sequence chr13-:115084360:115084375 ...
  >>> DONE searching in sequence chr13-:115084360:115084375!
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 in sequence chr13+:27629413:27629420:chr13-:27629399:27629417!
  >>> Finding all hits in sequence chr13+:39262920:39262939:chr13-:39262918:39262918 ...
  >>> DONE searching in sequence chr13+:39262920:39262939:chr13-:39262918:39262918!
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 in sequence chr13+:27629413:27629420:chr13-:27629400:27629404!
  >>> Finding all hits in sequence chr13+:39262927:39262939:chr13-:39262918:39262920 ...
  >>> DONE searching in sequence chr13+:39262927:39262939:chr13-:39262918:39262920!
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 
147.013   2.336 151.185