| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:05 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 803/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicAlignments 1.36.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the GenomicAlignments package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicAlignments.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. |
| Package: GenomicAlignments |
| Version: 1.36.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicAlignments_1.36.0.tar.gz |
| StartedAt: 2023-10-16 02:03:03 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 02:14:28 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 684.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicAlignments.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicAlignments_1.36.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GenomicAlignments.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* this is package ‘GenomicAlignments’ version ‘1.36.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'Rsamtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GenomicAlignments’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since
Cannot process chunk/lines:
version 1.18.0
Cannot process chunk/lines:
No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since
Cannot process chunk/lines:
version 1.16.0
Cannot process chunk/lines:
The first version of GenomicAlignments was included in Bioconductor 2.14.
Cannot process chunk/lines:
The package was created from existing code in IRanges, ShortRead,
Cannot process chunk/lines:
Rsamtools and GenomicRanges.
* 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
':::' calls which should be '::':
‘S4Vectors:::makeClassinfoRowForCompactPrinting’
‘S4Vectors:::makePrettyMatrixForCompactPrinting’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘Rsamtools:::.BamViews_delegate’ ‘Rsamtools:::.findMateWithinGroups’
‘Rsamtools:::.load_bamcols_from_scanBam_res’
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 ... OK
* checking Rd files ... WARNING
checkRd: (5) GAlignmentPairs-class.Rd:90-94: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:102-133: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:134-137: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:138-143: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:144-160: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:161-172: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:173-179: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:180-183: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:184-188: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:189-193: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:194-203: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:204-210: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:211-216: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:217-222: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:223-232: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:240-244: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:252-257: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:258-264: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:272-298: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:299-328: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:329-336: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:337-340: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:348-359: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:148-154: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:162-165: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:166-171: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:172-179: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:180-183: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:184-190: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:191-195: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:196-202: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:203-213: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:214-221: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:222-227: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:228-232: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:233-241: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:242-248: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:249-254: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:255-260: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:261-270: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:278-292: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:293-335: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:336-344: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:351-357: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:365-369: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:375-381: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:388-400: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:67-70: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:78-81: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:82-85: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:86-90: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:91-94: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:95-99: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:100-105: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:106-112: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:113-118: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:119-123: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:124-129: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:130-134: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:135-139: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:140-146: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:147-152: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:153-158: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:170-187: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:188-206: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:207-215: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:216-222: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:223-228: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:236-240: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:241-244: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:245-250: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:256-262: \item in \describe must have non-empty label
checkRd: (5) GappedReads-class.Rd:40-44: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:133-137: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:138-155: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:156-182: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:183-185: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:186-192: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:200-204: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:213-227: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:228-235: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:236-245: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:246-261: \item in \describe must have non-empty label
checkRd: (5) summarizeOverlaps-methods.Rd:226-246: \item in \describe must have non-empty label
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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
readGAlignments 24.522 5.152 37.799
junctions-methods 21.784 2.236 30.680
summarizeOverlaps-methods 14.384 4.054 22.829
coordinate-mapping-methods 13.716 0.450 17.730
sequenceLayer 11.075 2.290 17.982
findSpliceOverlaps-methods 9.201 0.274 11.979
stackStringsFromGAlignments 7.358 0.411 10.205
GAlignmentsList-class 4.623 0.139 6.070
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/GenomicAlignments.Rcheck/00check.log’
for details.
GenomicAlignments.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicAlignments ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘GenomicAlignments’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cigar_utils.c -o cigar_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs ** R ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicAlignments)
GenomicAlignments.Rcheck/tests/run_unitTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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.
> require("GenomicAlignments") || stop("unable to load GenomicRanges package")
Loading required package: GenomicAlignments
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
Loading required package: stats4
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
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
[1] TRUE
> GenomicAlignments:::.test()
RUNIT TEST PROTOCOL -- Mon Oct 16 02:14:03 2023
***********************************************
Number of test functions: 42
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicAlignments RUnit Tests - 42 test functions, 0 errors, 0 failures
Number of test functions: 42
Number of errors: 0
Number of failures: 0
Warning message:
In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode, :
4 alignments with ambiguous pairing were dumped.
Use 'getDumpedAlignments()' to retrieve them from the dump environment.
>
> proc.time()
user system elapsed
53.742 3.210 72.322
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
| name | user | system | elapsed | |
| GAlignmentPairs-class | 1.763 | 0.203 | 2.518 | |
| GAlignments-class | 0.680 | 0.036 | 0.916 | |
| GAlignmentsList-class | 4.623 | 0.139 | 6.070 | |
| GappedReads-class | 0.179 | 0.008 | 0.234 | |
| OverlapEncodings-class | 2.398 | 0.039 | 3.078 | |
| cigar-utils | 0.425 | 0.027 | 0.603 | |
| coordinate-mapping-methods | 13.716 | 0.450 | 17.730 | |
| coverage-methods | 3.694 | 0.230 | 4.958 | |
| encodeOverlaps-methods | 0.071 | 0.005 | 0.096 | |
| findCompatibleOverlaps-methods | 2.169 | 0.124 | 2.909 | |
| findMateAlignment | 0.302 | 0.017 | 0.416 | |
| findOverlaps-methods | 0.959 | 0.017 | 1.244 | |
| findSpliceOverlaps-methods | 9.201 | 0.274 | 11.979 | |
| intra-range-methods | 0.636 | 0.029 | 0.836 | |
| junctions-methods | 21.784 | 2.236 | 30.680 | |
| pileLettersAt | 1.260 | 0.041 | 1.626 | |
| readGAlignments | 24.522 | 5.152 | 37.799 | |
| sequenceLayer | 11.075 | 2.290 | 17.982 | |
| setops-methods | 0.244 | 0.007 | 0.343 | |
| stackStringsFromGAlignments | 7.358 | 0.411 | 10.205 | |
| summarizeOverlaps-methods | 14.384 | 4.054 | 22.829 | |