| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-10 10:04:27 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
|
To the developers/maintainers of the Biostrings package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Biostrings.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 212/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Biostrings 2.69.0 (landing page) Hervé Pagès
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: Biostrings |
| Version: 2.69.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Biostrings_2.69.0.tar.gz |
| StartedAt: 2023-05-09 10:08:17 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 10:21:44 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 807.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Biostrings.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Biostrings.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Biostrings_2.69.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Biostrings.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘Biostrings/DESCRIPTION’ ... OK
* this is package ‘Biostrings’ version ‘2.69.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biostrings’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 14.6Mb
sub-directories of 1Mb or more:
R 1.7Mb
extdata 11.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’
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 ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (5) AAString-class.Rd:74-78: \item in \describe must have non-empty label
checkRd: (5) AAString-class.Rd:86-92: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:87-90: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:91-96: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:97-99: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:100-103: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:104-107: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:108-111: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:112-116: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:117-121: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:122-125: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:126-129: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:130-133: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:134-137: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:138-141: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:147-151: \item in \describe must have non-empty label
checkRd: (5) AlignedXStringSet-class.Rd:152-156: \item in \describe must have non-empty label
checkRd: (5) DNAString-class.Rd:57-61: \item in \describe must have non-empty label
checkRd: (5) DNAString-class.Rd:69-75: \item in \describe must have non-empty label
checkRd: (5) InDel-class.Rd:32-35: \item in \describe must have non-empty label
checkRd: (5) InDel-class.Rd:36-39: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:49-52: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:53-56: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:57-61: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:62-66: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:67-71: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:79-83: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:91-99: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:110-115: \item in \describe must have non-empty label
checkRd: (5) MIndex-class.Rd:116-119: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:113-116: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:117-122: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:123-140: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:141-145: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:146-152: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:160-164: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:165-168: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:169-172: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:180-185: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:193-197: \item in \describe must have non-empty label
checkRd: (5) MaskedXString-class.Rd:198-203: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:157-161: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:162-167: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:168-178: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:179-189: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:190-200: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:201-216: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:217-220: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:221-224: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:225-228: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:229-232: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:233-236: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:237-240: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:241-244: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:245-249: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:250-253: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:261-267: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:268-274: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:275-282: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:290-298: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:299-304: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:305-312: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:313-320: \item in \describe must have non-empty label
checkRd: (5) MultipleAlignment-class.Rd:321-337: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:241-244: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:245-249: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:250-253: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:254-257: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:258-261: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:262-269: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:270-273: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:282-285: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:294-297: \item in \describe must have non-empty label
checkRd: (5) PDict-class.Rd:298-301: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:154-160: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:161-165: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:166-169: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:177-180: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:181-187: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:188-193: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:202-210: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:211-214: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:215-218: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:219-222: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:230-234: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:235-238: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:239-243: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:244-250: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:258-262: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:263-268: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:269-274: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:275-279: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:280-283: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:284-289: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:295-299: \item in \describe must have non-empty label
checkRd: (5) PairwiseAlignments-class.Rd:300-304: \item in \describe must have non-empty label
checkRd: (5) QualityScaledXStringSet-class.Rd:111-114: \item in \describe must have non-empty label
checkRd: (5) QualityScaledXStringSet-class.Rd:115-119: \item in \describe must have non-empty label
checkRd: (5) QualityScaledXStringSet-class.Rd:120-123: \item in \describe must have non-empty label
checkRd: (5) QualityScaledXStringSet-class.Rd:124-129: \item in \describe must have non-empty label
checkRd: (5) QualityScaledXStringSet-class.Rd:130-133: \item in \describe must have non-empty label
checkRd: (5) QualityScaledXStringSet-class.Rd:143-146: \item in \describe must have non-empty label
checkRd: (5) RNAString-class.Rd:55-59: \item in \describe must have non-empty label
checkRd: (5) RNAString-class.Rd:67-73: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:94-98: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:106-111: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:112-115: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:123-126: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:127-130: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:138-148: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:156-169: \item in \describe must have non-empty label
checkRd: (5) XString-class.Rd:170-173: \item in \describe must have non-empty label
checkRd: (5) XStringPartialMatches-class.Rd:32-35: \item in \describe must have non-empty label
checkRd: (5) XStringPartialMatches-class.Rd:36-39: \item in \describe must have non-empty label
checkRd: (5) XStringPartialMatches-class.Rd:49-54: \item in \describe must have non-empty label
checkRd: (-1) XStringQuality-class.Rd:86: Escaped LaTeX specials: \#
checkRd: (5) XStringQuality-class.Rd:106-109: \item in \describe must have non-empty label
checkRd: (5) XStringQuality-class.Rd:111-115: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:116-118: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:119-121: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:122-124: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:135-138: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:139-145: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:146-155: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:156-162: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:163-166: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:176-193: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:194-204: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:205-215: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:216-221: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:231-234: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:235-238: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:239-242: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:251-254: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:255-258: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:259-262: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:263-266: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:275-280: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:281-286: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:287-290: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:291-298: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:299-302: \item in \describe must have non-empty label
checkRd: (5) XStringSet-class.Rd:303-311: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:55-65: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:66-72: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:80-85: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:86-90: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:91-94: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:95-98: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:106-109: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:110-113: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:122-126: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:127-131: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:141-143: \item in \describe must have non-empty label
checkRd: (5) XStringSet-comparison.Rd:144-146: \item in \describe must have non-empty label
checkRd: (5) XStringViews-class.Rd:73-77: \item in \describe must have non-empty label
checkRd: (5) XStringViews-class.Rd:87-93: \item in \describe must have non-empty label
checkRd: (5) XStringViews-class.Rd:103-117: \item in \describe must have non-empty label
checkRd: (5) XStringViews-class.Rd:118-121: \item in \describe must have non-empty label
checkRd: (5) XStringViews-class.Rd:122-131: \item in \describe must have non-empty label
checkRd: (5) XStringViews-class.Rd:136-143: \item in \describe must have non-empty label
checkRd: (5) XStringViews-class.Rd:144-147: \item in \describe must have non-empty label
checkRd: (5) injectHardMask.Rd:58-61: \item in \describe must have non-empty label
checkRd: (5) injectHardMask.Rd:62-70: \item in \describe must have non-empty label
checkRd: (5) injectHardMask.Rd:71-74: \item in \describe must have non-empty label
checkRd: (-1) matchLRPatterns.Rd:65: Escaped LaTeX specials: \_ \_
checkRd: (-1) matchProbePair.Rd:53: Escaped LaTeX specials: \_ \_
checkRd: (-1) matchProbePair.Rd:54: Escaped LaTeX specials: \_ \_
checkRd: (-1) matchProbePair.Rd:55: Escaped LaTeX specials: \_ \_
checkRd: (-1) matchProbePair.Rd:56: Escaped LaTeX specials: \_ \_
checkRd: (-1) phiX174Phage.Rd:18: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘strsplit’ ‘twoWayAlphabetFrequency’
Undocumented S4 methods:
generic 'match' and siglist 'Vector,XStringSet'
generic 'match' and siglist 'XStringSet,Vector'
generic 'match' and siglist 'XStringSet,vector'
generic 'match' and siglist 'vector,XStringSet'
generic 'parallel_slot_names' and siglist 'ByPos_MIndex'
generic 'parallel_slot_names' and siglist 'MIndex'
generic 'pcompare' and siglist 'Vector,XStringSet'
generic 'pcompare' and siglist 'XStringSet,Vector'
generic 'pcompare' and siglist 'XStringSet,vector'
generic 'pcompare' and siglist 'vector,XStringSet'
generic 'relistToClass' and siglist 'XString'
generic 'strsplit' and siglist 'XStringSet'
generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
generic 'unstrsplit' and siglist 'XStringSet'
generic 'unstrsplit' and siglist 'XStringSetList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
matchPDict-exact 354.071 2.220 356.297
matchPDict-inexact 57.536 0.416 57.952
findPalindromes 45.000 0.072 45.077
XStringSet-class 14.180 0.488 14.677
XStringSet-io 9.267 0.242 9.513
matchPattern 6.142 0.184 6.326
* 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 ...
‘matchprobes.Rmd’ using ‘UTF-8’... OK
‘Biostrings2Classes.Rnw’ using ‘UTF-8’... OK
‘BiostringsQuickOverview.Rnw’ using ‘UTF-8’... OK
‘MultipleAlignments.Rnw’ using ‘UTF-8’... OK
‘PairwiseAlignments.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/Biostrings.Rcheck/00check.log’
for details.
Biostrings.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Biostrings ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘Biostrings’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c BAB_class.c -o BAB_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c BitMatrix.c -o BitMatrix.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c MIndex_class.c -o MIndex_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c SparseList_utils.c -o SparseList_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c XStringSet_class.c -o XStringSet_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c XString_class.c -o XString_class.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c align_utils.c -o align_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c find_palindromes.c -o find_palindromes.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c gtestsim.c -o gtestsim.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c inject_code.c -o inject_code.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c letter_frequency.c -o letter_frequency.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_PWM.c -o match_PWM.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_pattern.c -o match_pattern.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_pattern_indels.c -o match_pattern_indels.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_pdict.c -o match_pdict.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_pdict_utils.c -o match_pdict_utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c match_reporting.c -o match_reporting.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c matchprobes.c -o matchprobes.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c pmatchPattern.c -o pmatchPattern.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c read_fasta_files.c -o read_fasta_files.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c read_fastq_files.c -o read_fastq_files.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c replaceAt.c -o replaceAt.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c replace_letter_at.c -o replace_letter_at.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c strutils.c -o strutils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c translate.c -o translate.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -c xscat.c -o xscat.o gcc -shared -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-Biostrings/00new/Biostrings/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet” Creating a new generic function for ‘strsplit’ in package ‘Biostrings’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’ Creating a new generic function for ‘pattern’ in package ‘Biostrings’ Creating a new generic function for ‘offset’ in package ‘Biostrings’ ** 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 (Biostrings)
Biostrings.Rcheck/tests/run_unitTests.Rout
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> require("Biostrings") || stop("unable to load Biostrings package")
Loading required package: Biostrings
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 objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
[1] TRUE
> Biostrings:::.test()
RUNIT TEST PROTOCOL -- Tue May 9 10:19:13 2023
***********************************************
Number of test functions: 41
Number of errors: 0
Number of failures: 0
1 Test Suite :
Biostrings RUnit Tests - 41 test functions, 0 errors, 0 failures
Number of test functions: 41
Number of errors: 0
Number of failures: 0
Warning messages:
1: In XStringSet("DNA", x, start = start, end = end, width = width, :
metadata columns on input DNAStringSet object were dropped
2: In XStringSet("DNA", x, start = start, end = end, width = width, :
metadata columns on input DNAStringSet object were dropped
3: In XStringSet("DNA", x, start = start, end = end, width = width, :
metadata columns on input DNAStringSet object were dropped
>
> proc.time()
user system elapsed
11.079 0.356 11.423
Biostrings.Rcheck/Biostrings-Ex.timings
| name | user | system | elapsed | |
| AAString-class | 0.004 | 0.000 | 0.004 | |
| AMINO_ACID_CODE | 0.002 | 0.000 | 0.002 | |
| AlignedXStringSet-class | 0.070 | 0.004 | 0.073 | |
| DNAString-class | 0.004 | 0.000 | 0.004 | |
| GENETIC_CODE | 0.012 | 0.000 | 0.011 | |
| HNF4alpha | 0.024 | 0.000 | 0.025 | |
| IUPAC_CODE_MAP | 0.155 | 0.012 | 0.167 | |
| MIndex-class | 0.001 | 0.000 | 0.000 | |
| MaskedXString-class | 0.232 | 0.024 | 0.258 | |
| MultipleAlignment-class | 1.517 | 0.012 | 1.531 | |
| PDict-class | 4.513 | 0.092 | 4.610 | |
| PairwiseAlignments-class | 0.692 | 0.000 | 0.692 | |
| PairwiseAlignments-io | 2.789 | 0.068 | 2.856 | |
| QualityScaledXStringSet-class | 0.167 | 0.004 | 0.174 | |
| RNAString-class | 0.009 | 0.000 | 0.008 | |
| XString-class | 0.006 | 0.004 | 0.010 | |
| XStringQuality-class | 0.175 | 0.000 | 0.175 | |
| XStringSet-class | 14.180 | 0.488 | 14.677 | |
| XStringSet-comparison | 3.327 | 0.108 | 3.437 | |
| XStringSet-io | 9.267 | 0.242 | 9.513 | |
| XStringSetList-class | 0.292 | 0.000 | 0.291 | |
| XStringViews-class | 0.136 | 0.004 | 0.140 | |
| align-utils | 0.045 | 0.000 | 0.045 | |
| chartr | 0.708 | 0.012 | 0.722 | |
| detail | 0.337 | 0.012 | 0.349 | |
| dinucleotideFrequencyTest | 0.013 | 0.000 | 0.013 | |
| findPalindromes | 45.000 | 0.072 | 45.077 | |
| getSeq | 0.057 | 0.016 | 0.073 | |
| gregexpr2 | 0.001 | 0.000 | 0.001 | |
| injectHardMask | 0.043 | 0.008 | 0.051 | |
| letter | 0.024 | 0.003 | 0.026 | |
| letterFrequency | 0.991 | 0.092 | 1.083 | |
| longestConsecutive | 0 | 0 | 0 | |
| lowlevel-matching | 0.554 | 0.024 | 0.578 | |
| maskMotif | 1.523 | 0.024 | 1.550 | |
| match-utils | 0.024 | 0.004 | 0.027 | |
| matchLRPatterns | 0.558 | 0.020 | 0.581 | |
| matchPDict-exact | 354.071 | 2.220 | 356.297 | |
| matchPDict-inexact | 57.536 | 0.416 | 57.952 | |
| matchPWM | 2.530 | 0.024 | 2.555 | |
| matchPattern | 6.142 | 0.184 | 6.326 | |
| matchProbePair | 1.590 | 0.012 | 1.601 | |
| matchprobes | 0.298 | 0.008 | 0.306 | |
| misc | 0.017 | 0.000 | 0.017 | |
| needwunsQS | 0 | 0 | 0 | |
| nucleotideFrequency | 0.713 | 0.072 | 0.784 | |
| padAndClip | 0.588 | 0.008 | 0.596 | |
| pairwiseAlignment | 0.802 | 0.012 | 0.814 | |
| phiX174Phage | 0.497 | 0.028 | 0.526 | |
| pid | 0.48 | 0.02 | 0.50 | |
| replaceAt | 2.671 | 0.012 | 2.683 | |
| replaceLetterAt | 0.814 | 0.020 | 0.835 | |
| reverseComplement | 1.310 | 0.008 | 1.318 | |
| seqinfo-methods | 0.724 | 0.004 | 0.728 | |
| stringDist | 3.961 | 0.004 | 3.965 | |
| substitution_matrices | 1.058 | 0.004 | 1.062 | |
| toComplex | 0.001 | 0.000 | 0.001 | |
| translate | 1.411 | 0.008 | 1.419 | |
| trimLRPatterns | 0.074 | 0.000 | 0.075 | |
| xscat | 1.313 | 0.012 | 1.325 | |
| yeastSEQCHR1 | 0.004 | 0.000 | 0.004 | |