| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:44 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 819/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicAlignments 1.38.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: GenomicAlignments |
| Version: 1.38.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenomicAlignments_1.38.0.tar.gz |
| StartedAt: 2023-11-02 10:48:59 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 10:54:34 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 335.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomicAlignments.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenomicAlignments_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicAlignments.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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
* using option ‘--no-vignettes’
* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* this is package ‘GenomicAlignments’ version ‘1.38.0’
* 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: ‘gcc (GCC) 10.3.1’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomicAlignments-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readGAlignments
> ### Title: Reading genomic alignments from a file
> ### Aliases: readGAlignments readGAlignments,BamFile-method
> ### readGAlignments,character-method readGAlignments,BamViews-method
> ### readGAlignmentPairs readGAlignmentPairs,BamFile-method
> ### readGAlignmentPairs,character-method readGAlignmentsList
> ### readGAlignmentsList,BamFile-method
> ### readGAlignmentsList,character-method readGappedReads
> ### readGappedReads,BamFile-method readGappedReads,character-method
> ### Keywords: manip
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## A. readGAlignments()
> ## ---------------------------------------------------------------------
>
> ## Simple use:
> bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
+ mustWork=TRUE)
> gal1 <- readGAlignments(bamfile)
> gal1
GAlignments object with 3271 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] seq1 + 36M 36 1 36 36
[2] seq1 + 35M 35 3 37 35
[3] seq1 + 35M 35 5 39 35
[4] seq1 + 36M 36 6 41 36
[5] seq1 + 35M 35 9 43 35
... ... ... ... ... ... ... ...
[3267] seq2 + 35M 35 1524 1558 35
[3268] seq2 + 35M 35 1524 1558 35
[3269] seq2 - 35M 35 1528 1562 35
[3270] seq2 - 35M 35 1532 1566 35
[3271] seq2 - 35M 35 1533 1567 35
njunc
<integer>
[1] 0
[2] 0
[3] 0
[4] 0
[5] 0
... ...
[3267] 0
[3268] 0
[3269] 0
[3270] 0
[3271] 0
-------
seqinfo: 2 sequences from an unspecified genome
> names(gal1)
NULL
>
> ## Using the 'use.names' arg:
> gal2 <- readGAlignments(bamfile, use.names=TRUE)
> gal2
GAlignments object with 3271 alignments and 0 metadata columns:
seqnames strand cigar qwidth start
<Rle> <Rle> <character> <integer> <integer>
B7_591:4:96:693:509 seq1 + 36M 36 1
EAS54_65:7:152:368:113 seq1 + 35M 35 3
EAS51_64:8:5:734:57 seq1 + 35M 35 5
B7_591:1:289:587:906 seq1 + 36M 36 6
EAS56_59:8:38:671:758 seq1 + 35M 35 9
... ... ... ... ... ...
EAS56_63:4:141:9:811 seq2 + 35M 35 1524
EAS114_30:6:277:397:932 seq2 + 35M 35 1524
EAS139_11:7:50:1229:1313 seq2 - 35M 35 1528
EAS54_65:3:320:20:250 seq2 - 35M 35 1532
EAS114_26:7:37:79:581 seq2 - 35M 35 1533
end width njunc
<integer> <integer> <integer>
B7_591:4:96:693:509 36 36 0
EAS54_65:7:152:368:113 37 35 0
EAS51_64:8:5:734:57 39 35 0
B7_591:1:289:587:906 41 36 0
EAS56_59:8:38:671:758 43 35 0
... ... ... ...
EAS56_63:4:141:9:811 1558 35 0
EAS114_30:6:277:397:932 1558 35 0
EAS139_11:7:50:1229:1313 1562 35 0
EAS54_65:3:320:20:250 1566 35 0
EAS114_26:7:37:79:581 1567 35 0
-------
seqinfo: 2 sequences from an unspecified genome
> head(names(gal2))
[1] "B7_591:4:96:693:509" "EAS54_65:7:152:368:113" "EAS51_64:8:5:734:57"
[4] "B7_591:1:289:587:906" "EAS56_59:8:38:671:758" "EAS56_61:6:18:467:281"
>
> ## Using the 'param' arg to drop PCR or optical duplicates as well as
> ## secondary alignments, and to load additional BAM fields:
> param <- ScanBamParam(flag=scanBamFlag(isDuplicate=FALSE,
+ isSecondaryAlignment=FALSE),
+ what=c("qual", "flag"))
> gal3 <- readGAlignments(bamfile, param=param)
> gal3
GAlignments object with 3271 alignments and 2 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] seq1 + 36M 36 1 36 36
[2] seq1 + 35M 35 3 37 35
[3] seq1 + 35M 35 5 39 35
[4] seq1 + 36M 36 6 41 36
[5] seq1 + 35M 35 9 43 35
... ... ... ... ... ... ... ...
[3267] seq2 + 35M 35 1524 1558 35
[3268] seq2 + 35M 35 1524 1558 35
[3269] seq2 - 35M 35 1528 1562 35
[3270] seq2 - 35M 35 1532 1566 35
[3271] seq2 - 35M 35 1533 1567 35
njunc | qual flag
<integer> | <PhredQuality> <integer>
[1] 0 | <<<<<<<<<<...<<<<<;:<;7 73
[2] 0 | <<<<<<<<<<...9<<3/:<6): 73
[3] 0 | <<<<<<<<<<...<3;);3*8/5 137
[4] 0 | (-&----,--...,+-,),''*, 137
[5] 0 | <<<<<<<<<<...<<7<<;:<5% 137
... ... . ... ...
[3267] 0 | <<<;<<<<<<...<<<..));;. 137
[3268] 0 | <<<<<<<<<<...<<<:8(,0%( 73
[3269] 0 | <<<<,<&<7<...<<<<<<<<<< 83
[3270] 0 | +'''/<<<<7...<<<<<<<<<< 147
[3271] 0 | 3,,,===6==...========== 83
-------
seqinfo: 2 sequences from an unspecified genome
> mcols(gal3)
DataFrame with 3271 rows and 2 columns
qual flag
<PhredQuality> <integer>
1 <<<<<<<<<<...<<<<<;:<;7 73
2 <<<<<<<<<<...9<<3/:<6): 73
3 <<<<<<<<<<...<3;);3*8/5 137
4 (-&----,--...,+-,),''*, 137
5 <<<<<<<<<<...<<7<<;:<5% 137
... ... ...
3267 <<<;<<<<<<...<<<..));;. 137
3268 <<<<<<<<<<...<<<:8(,0%( 73
3269 <<<<,<&<7<...<<<<<<<<<< 83
3270 +'''/<<<<7...<<<<<<<<<< 147
3271 3,,,===6==...========== 83
>
> ## Using the 'param' arg to load alignments from particular regions.
> which <- IRangesList(seq1=IRanges(1000, 1100),
+ seq2=IRanges(c(1546, 1555, 1567), width=10))
> param <- ScanBamParam(which=which)
> gal4 <- readGAlignments(bamfile, use.names=TRUE, param=param)
> gal4
GAlignments object with 205 alignments and 0 metadata columns:
seqnames strand cigar qwidth start
<Rle> <Rle> <character> <integer> <integer>
EAS114_26:7:86:308:648 seq1 + 35M 35 970
EAS56_65:8:206:563:262 seq1 + 35M 35 971
EAS56_65:6:82:822:767 seq1 + 35M 35 972
EAS56_57:5:207:926:427 seq1 + 35M 35 973
EAS51_62:7:144:28:475 seq1 + 35M 35 974
... ... ... ... ... ...
EAS114_30:6:277:397:932 seq2 + 35M 35 1524
EAS139_11:7:50:1229:1313 seq2 - 35M 35 1528
EAS54_65:3:320:20:250 seq2 - 35M 35 1532
EAS114_26:7:37:79:581 seq2 - 35M 35 1533
EAS114_26:7:37:79:581 seq2 - 35M 35 1533
end width njunc
<integer> <integer> <integer>
EAS114_26:7:86:308:648 1004 35 0
EAS56_65:8:206:563:262 1005 35 0
EAS56_65:6:82:822:767 1006 35 0
EAS56_57:5:207:926:427 1007 35 0
EAS51_62:7:144:28:475 1008 35 0
... ... ... ...
EAS114_30:6:277:397:932 1558 35 0
EAS139_11:7:50:1229:1313 1562 35 0
EAS54_65:3:320:20:250 1566 35 0
EAS114_26:7:37:79:581 1567 35 0
EAS114_26:7:37:79:581 1567 35 0
-------
seqinfo: 2 sequences from an unspecified genome
>
> ## IMPORTANT NOTE: A given record is loaded one time for each region
> ## it overlaps with. We call this "duplicated record selection" (this
> ## is a scanBam() feature, readGAlignments() is based on scanBam()):
> which <- IRangesList(seq2=IRanges(c(1555, 1567), width=10))
> param <- ScanBamParam(which=which)
> gal5 <- readGAlignments(bamfile, use.names=TRUE, param=param)
> gal5 # record EAS114_26:7:37:79:581 was loaded twice
GAlignments object with 9 alignments and 0 metadata columns:
seqnames strand cigar qwidth start
<Rle> <Rle> <character> <integer> <integer>
EAS54_71:8:105:854:975 seq2 - 33M 33 1523
EAS51_62:4:187:907:145 seq2 - 35M 35 1524
EAS54_71:4:284:269:882 seq2 + 34M 34 1524
EAS56_63:4:141:9:811 seq2 + 35M 35 1524
EAS114_30:6:277:397:932 seq2 + 35M 35 1524
EAS139_11:7:50:1229:1313 seq2 - 35M 35 1528
EAS54_65:3:320:20:250 seq2 - 35M 35 1532
EAS114_26:7:37:79:581 seq2 - 35M 35 1533
EAS114_26:7:37:79:581 seq2 - 35M 35 1533
end width njunc
<integer> <integer> <integer>
EAS54_71:8:105:854:975 1555 33 0
EAS51_62:4:187:907:145 1558 35 0
EAS54_71:4:284:269:882 1557 34 0
EAS56_63:4:141:9:811 1558 35 0
EAS114_30:6:277:397:932 1558 35 0
EAS139_11:7:50:1229:1313 1562 35 0
EAS54_65:3:320:20:250 1566 35 0
EAS114_26:7:37:79:581 1567 35 0
EAS114_26:7:37:79:581 1567 35 0
-------
seqinfo: 2 sequences from an unspecified genome
>
> ## This becomes clearer if we use 'with.which_label=TRUE' to identify
> ## the region in 'which' where each element in 'gal5' originates from.
> gal5 <- readGAlignments(bamfile, use.names=TRUE, param=param,
+ with.which_label=TRUE)
> gal5
GAlignments object with 9 alignments and 1 metadata column:
seqnames strand cigar qwidth start
<Rle> <Rle> <character> <integer> <integer>
EAS54_71:8:105:854:975 seq2 - 33M 33 1523
EAS51_62:4:187:907:145 seq2 - 35M 35 1524
EAS54_71:4:284:269:882 seq2 + 34M 34 1524
EAS56_63:4:141:9:811 seq2 + 35M 35 1524
EAS114_30:6:277:397:932 seq2 + 35M 35 1524
EAS139_11:7:50:1229:1313 seq2 - 35M 35 1528
EAS54_65:3:320:20:250 seq2 - 35M 35 1532
EAS114_26:7:37:79:581 seq2 - 35M 35 1533
EAS114_26:7:37:79:581 seq2 - 35M 35 1533
end width njunc | which_label
<integer> <integer> <integer> | <Rle>
EAS54_71:8:105:854:975 1555 33 0 | seq2:1555-1564
EAS51_62:4:187:907:145 1558 35 0 | seq2:1555-1564
EAS54_71:4:284:269:882 1557 34 0 | seq2:1555-1564
EAS56_63:4:141:9:811 1558 35 0 | seq2:1555-1564
EAS114_30:6:277:397:932 1558 35 0 | seq2:1555-1564
EAS139_11:7:50:1229:1313 1562 35 0 | seq2:1555-1564
EAS54_65:3:320:20:250 1566 35 0 | seq2:1555-1564
EAS114_26:7:37:79:581 1567 35 0 | seq2:1555-1564
EAS114_26:7:37:79:581 1567 35 0 | seq2:1567-1576
-------
seqinfo: 2 sequences from an unspecified genome
>
> ## Not surprisingly, we also get "duplicated record selection" when
> ## 'which' contains repeated or overlapping regions. Using the same
> ## regions as we did for 'gal4' above, except that now we're
> ## repeating the region on seq1:
> which <- IRangesList(seq1=rep(IRanges(1000, 1100), 2),
+ seq2=IRanges(c(1546, 1555, 1567), width=10))
> param <- ScanBamParam(which=which)
> gal4b <- readGAlignments(bamfile, use.names=TRUE, param=param)
> length(gal4b) # > length(gal4), because all the records overlapping
[1] 366
> # with bases 1000 to 1100 on seq1 are now duplicated
>
> ## The "duplicated record selection" will artificially increase the
> ## coverage or affect other downstream results. It can be mitigated
> ## (but not completely eliminated) by first "reducing" the set of
> ## regions:
> which <- reduce(which)
> which
IRangesList object of length 2:
$seq1
IRanges object with 1 range and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1000 1100 101
$seq2
IRanges object with 2 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1546 1564 19
[2] 1567 1576 10
> param <- ScanBamParam(which=which)
> gal4c <- readGAlignments(bamfile, use.names=TRUE, param=param)
> length(gal4c) # < length(gal4), because the 2 first original regions
[1] 197
> # on seq2 were merged into a single one
>
> ## Note that reducing the set of regions didn't completely eliminate
> ## "duplicated record selection". Records that overlap the 2 reduced
> ## regions on seq2 (which$seq2) are loaded twice (like for 'gal5'
> ## above). See example D. below for how to completely eliminate
> ## "duplicated record selection".
>
> ## Using the 'param' arg to load tags. Except for MF and Aq, the tags
> ## specified below are predefined tags (see the SAM Spec for the list
> ## of predefined tags and their meaning).
> param <- ScanBamParam(tag=c("MF", "Aq", "NM", "UQ", "H0", "H1"),
+ what="isize")
> gal6 <- readGAlignments(bamfile, param=param)
> mcols(gal6) # "tag" cols always after "what" cols
DataFrame with 3271 rows and 7 columns
isize MF Aq NM UQ H0 H1
<integer> <integer> <integer> <integer> <integer> <integer> <integer>
1 NA 18 73 0 0 1 0
2 NA 18 66 0 0 1 0
3 NA 18 66 0 0 1 0
4 NA 130 63 5 38 0 0
5 NA 18 72 0 0 1 0
... ... ... ... ... ... ... ...
3267 NA 32 0 3 47 2 27
3268 NA 32 0 3 42 2 85
3269 -187 18 0 1 11 3 7
3270 -200 18 6 2 24 1 2
3271 -219 18 27 2 23 0 1
>
> ## With a BamViews object:
> fls <- system.file("extdata", "ex1.bam", package="Rsamtools",
+ mustWork=TRUE)
> bv <- BamViews(fls,
+ bamSamples=DataFrame(info="test", row.names="ex1"),
+ auto.range=TRUE)
> ## Note that the "readGAlignments" method for BamViews objects
> ## requires the ShortRead package to be installed.
> aln <- readGAlignments(bv)
> aln
List of length 1
names(1): ex1
> aln[[1]]
GAlignments object with 3271 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] seq1 + 36M 36 1 36 36
[2] seq1 + 35M 35 3 37 35
[3] seq1 + 35M 35 5 39 35
[4] seq1 + 36M 36 6 41 36
[5] seq1 + 35M 35 9 43 35
... ... ... ... ... ... ... ...
[3267] seq2 + 35M 35 1524 1558 35
[3268] seq2 + 35M 35 1524 1558 35
[3269] seq2 - 35M 35 1528 1562 35
[3270] seq2 - 35M 35 1532 1566 35
[3271] seq2 - 35M 35 1533 1567 35
njunc
<integer>
[1] 0
[2] 0
[3] 0
[4] 0
[5] 0
... ...
[3267] 0
[3268] 0
[3269] 0
[3270] 0
[3271] 0
-------
seqinfo: 2 sequences from an unspecified genome
> aln[colnames(bv)]
List of length 1
names(1): ex1
> mcols(aln)
DataFrame with 1 row and 1 column
info
<character>
ex1 test
>
> ## ---------------------------------------------------------------------
> ## B. readGAlignmentPairs()
> ## ---------------------------------------------------------------------
> galp1 <- readGAlignmentPairs(bamfile)
> head(galp1)
GAlignmentPairs object with 6 pairs, strandMode=1, and 0 metadata columns:
seqnames strand : ranges -- ranges
<Rle> <Rle> : <IRanges> -- <IRanges>
[1] seq1 + : 36-70 -- 185-219
[2] seq1 + : 49-84 -- 224-259
[3] seq1 + : 51-85 -- 228-262
[4] seq1 + : 60-95 -- 224-259
[5] seq1 + : 60-94 -- 235-269
[6] seq1 + : 61-95 -- 248-282
-------
seqinfo: 2 sequences from an unspecified genome
> names(galp1)
NULL
>
> ## Here we use the 'param' arg to filter by proper pair, drop PCR /
> ## optical duplicates, and drop secondary alignments. Filtering by
> ## proper pair and dropping secondary alignments can help make the
> ## pairing algorithm run significantly faster:
> param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE,
+ isDuplicate=FALSE,
+ isSecondaryAlignment=FALSE))
> galp2 <- readGAlignmentPairs(bamfile, use.names=TRUE, param=param)
> galp2
GAlignmentPairs object with 1572 pairs, strandMode=1, and 0 metadata columns:
seqnames strand : ranges -- ranges
<Rle> <Rle> : <IRanges> -- <IRanges>
EAS54_61:4:143:69:578 seq1 + : 36-70 -- 185-219
B7_593:4:106:316:452 seq1 + : 49-84 -- 224-259
EAS54_65:3:321:311:983 seq1 + : 51-85 -- 228-262
B7_591:5:42:540:501 seq1 + : 60-95 -- 224-259
EAS192_3:5:223:142:410 seq1 + : 60-94 -- 235-269
... ... ... ... ... ... ...
EAS139_11:5:52:1278:1478 seq2 - : 1513-1547 -- 1322-1356
EAS1_97:4:274:287:423 seq2 - : 1515-1549 -- 1332-1366
EAS54_71:8:105:854:975 seq2 - : 1523-1555 -- 1354-1388
EAS139_11:7:50:1229:1313 seq2 - : 1528-1562 -- 1376-1410
EAS114_26:7:37:79:581 seq2 - : 1533-1567 -- 1349-1383
-------
seqinfo: 2 sequences from an unspecified genome
> head(galp2)
GAlignmentPairs object with 6 pairs, strandMode=1, and 0 metadata columns:
seqnames strand : ranges -- ranges
<Rle> <Rle> : <IRanges> -- <IRanges>
EAS54_61:4:143:69:578 seq1 + : 36-70 -- 185-219
B7_593:4:106:316:452 seq1 + : 49-84 -- 224-259
EAS54_65:3:321:311:983 seq1 + : 51-85 -- 228-262
B7_591:5:42:540:501 seq1 + : 60-95 -- 224-259
EAS192_3:5:223:142:410 seq1 + : 60-94 -- 235-269
EAS56_61:6:227:259:597 seq1 + : 61-95 -- 248-282
-------
seqinfo: 2 sequences from an unspecified genome
> head(names(galp2))
[1] "EAS54_61:4:143:69:578" "B7_593:4:106:316:452" "EAS54_65:3:321:311:983"
[4] "B7_591:5:42:540:501" "EAS192_3:5:223:142:410" "EAS56_61:6:227:259:597"
>
> ## ---------------------------------------------------------------------
> ## C. readGAlignmentsList()
> ## ---------------------------------------------------------------------
> library(pasillaBamSubset)
>
> ## 'file' as character.
> bam <- untreated3_chr4()
> galist1 <- readGAlignmentsList(bam)
> galist1[1:3]
GAlignmentsList object of length 3:
[[1]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 169 205 37
[2] chr4 - 37M 37 326 362 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[2]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 946 982 37
[2] chr4 - 37M 37 986 1022 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[3]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 943 979 37
[2] chr4 - 37M 37 1086 1122 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
> length(galist1)
[1] 96636
> table(elementNROWS(galist1))
1 2 3 4 5 6 7 8 9
18191 78297 69 60 7 8 2 1 1
>
> ## When 'file' is a BamFile, 'asMates' must be TRUE. If FALSE,
> ## the data are treated as single-end and each list element of the
> ## GAlignmentsList will be of length 1. For single-end data
> ## use readGAlignments().
> bamfile <- BamFile(bam, yieldSize=3, asMates=TRUE)
> readGAlignmentsList(bamfile)
GAlignmentsList object of length 3:
[[1]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 169 205 37
[2] chr4 - 37M 37 326 362 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[2]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 946 982 37
[2] chr4 - 37M 37 986 1022 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[3]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 943 979 37
[2] chr4 - 37M 37 1086 1122 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
>
> ## Use a 'param' to fine tune the results.
> param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE))
> galist2 <- readGAlignmentsList(bam, param=param)
> galist2[1:3]
GAlignmentsList object of length 3:
[[1]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 169 205 37
[2] chr4 - 37M 37 326 362 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[2]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 946 982 37
[2] chr4 - 37M 37 986 1022 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[3]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 943 979 37
[2] chr4 - 37M 37 1086 1122 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
> length(galist2)
[1] 45828
> table(elementNROWS(galist2))
2
45828
>
> ## For paired-end data, we can set the 'strandMode' parameter to
> ## infer the strand of a pair from the strand of the first and
> ## last alignments in the pair
> galist3 <- readGAlignmentsList(bam, param=param, strandMode=0)
> galist3[1:3]
GAlignmentsList object of length 3:
[[1]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 * 37M 37 169 205 37
[2] chr4 * 37M 37 326 362 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[2]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 * 37M 37 946 982 37
[2] chr4 * 37M 37 986 1022 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[3]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 * 37M 37 943 979 37
[2] chr4 * 37M 37 1086 1122 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
> galist4 <- readGAlignmentsList(bam, param=param, strandMode=1)
> galist4[1:3]
GAlignmentsList object of length 3:
[[1]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 169 205 37
[2] chr4 + 37M 37 326 362 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[2]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 946 982 37
[2] chr4 + 37M 37 986 1022 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[3]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 + 37M 37 943 979 37
[2] chr4 + 37M 37 1086 1122 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
> galist5 <- readGAlignmentsList(bam, param=param, strandMode=2)
> galist5[1:3]
GAlignmentsList object of length 3:
[[1]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 - 37M 37 169 205 37
[2] chr4 - 37M 37 326 362 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[2]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 - 37M 37 946 982 37
[2] chr4 - 37M 37 986 1022 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
[[3]]
GAlignments object with 2 alignments and 0 metadata columns:
seqnames strand cigar qwidth start end width
<Rle> <Rle> <character> <integer> <integer> <integer> <integer>
[1] chr4 - 37M 37 943 979 37
[2] chr4 - 37M 37 1086 1122 37
njunc
<integer>
[1] 0
[2] 0
-------
seqinfo: 8 sequences from an unspecified genome
>
> ## ---------------------------------------------------------------------
> ## D. COMPARING 4 STRATEGIES FOR LOADING THE ALIGNMENTS THAT OVERLAP
> ## WITH THE EXONIC REGIONS ON FLY CHROMMOSOME 4
> ## ---------------------------------------------------------------------
> library(pasillaBamSubset)
> bam <- untreated1_chr4()
>
> library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
> txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
> ex <- exons(txdb)
> seqlevels(ex, pruning.mode="coarse") <- "chr4"
> length(ex)
[1] 1002
>
> ## Some of the exons overlap with each other:
> isDisjoint(ex) # FALSE
[1] FALSE
> exonic_regions <- reduce(ex)
> isDisjoint(exonic_regions) # no more overlaps
[1] TRUE
> length(exonic_regions)
[1] 786
>
> ## Strategy #1: slow and loads a lot of records more than once (see
> ## "duplicated record selection" in example A. above).
> param1 <- ScanBamParam(which=ex)
> gal1 <- readGAlignments(bam, param=param1)
* 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 ERROR, 1 WARNING, 5 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicAlignments.Rcheck/00check.log’
for details.
GenomicAlignments.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL GenomicAlignments
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function ‘cigar_ranges’:
cigar_utils.c:676:9: warning: ‘f_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
676 | f_elt++;
| ~~~~~^~
cigar_utils.c:674:22: warning: ‘range_buf1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
674 | *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:674:16: warning: ‘breakpoint’ may be used uninitialized in this function [-Wmaybe-uninitialized]
674 | *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
| ~~~~~~~~~~~^~~
cigar_utils.c:626:8: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
626 | if (*flag_elt == NA_INTEGER) {
| ^~~~~~~~~
cigar_utils.c: In function ‘cigar_width’:
cigar_utils.c:708:8: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
708 | if (*flag_elt == NA_INTEGER) {
| ^~~~~~~~~
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:879:2: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
879 | for (offset = Loffset; offset <= Roffset; offset += n) {
| ^~~
cigar_utils.c:854:15: note: ‘Roffset’ was declared here
854 | int Loffset, Roffset, buf_offset;
| ^~~~~~~
cigar_utils.c:881:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
881 | if (offset == Loffset)
| ^
cigar_utils.c:854:6: note: ‘Loffset’ was declared here
854 | int Loffset, Roffset, buf_offset;
| ^~~~~~~
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1074:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1074 | if (offset == Roffset)
| ^
cigar_utils.c:1045:15: note: ‘Roffset’ was declared here
1045 | int Loffset, Roffset, buf_offset;
| ^~~~~~~
cigar_utils.c:1072:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1072 | if (offset == Loffset)
| ^
cigar_utils.c:1045:6: note: ‘Loffset’ was declared here
1045 | int Loffset, Roffset, buf_offset;
| ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include -fPIC -g -O2 -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-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: 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.
> 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 -- Thu Nov 2 10:54:29 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
35.210 2.492 38.044
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
| name | user | system | elapsed | |
| GAlignmentPairs-class | 1.807 | 0.140 | 1.950 | |
| GAlignments-class | 0.417 | 0.040 | 0.458 | |
| GAlignmentsList-class | 2.448 | 0.132 | 2.593 | |
| GappedReads-class | 0.118 | 0.000 | 0.118 | |
| OverlapEncodings-class | 1.367 | 0.028 | 1.398 | |
| cigar-utils | 0.311 | 0.004 | 0.317 | |
| coordinate-mapping-methods | 10.220 | 0.115 | 10.388 | |
| coverage-methods | 3.579 | 0.012 | 3.603 | |
| encodeOverlaps-methods | 0.038 | 0.000 | 0.039 | |
| findCompatibleOverlaps-methods | 1.201 | 0.012 | 1.235 | |
| findMateAlignment | 0.158 | 0.008 | 0.168 | |
| findOverlaps-methods | 0.566 | 0.000 | 0.567 | |
| findSpliceOverlaps-methods | 7.067 | 0.068 | 7.155 | |
| intra-range-methods | 0.407 | 0.008 | 0.417 | |
| junctions-methods | 15.642 | 1.572 | 18.195 | |
| pileLettersAt | 1.900 | 0.052 | 1.959 | |