H. Pagès
| Snapshot Date: 2023-03-23 14:00:15 -0400 (Thu, 23 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/Biostrings |
| git_branch: devel |
| git_last_commit: c94e8fb |
| git_last_commit_date: 2022-11-01 10:36:29 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-24 11:05:07 -0400 (Fri, 24 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4546 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4307 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4299 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 214/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Biostrings 2.67.0 (landing page) H. Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: Biostrings |
| Version: 2.67.0 |
| 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_2.67.0.tar.gz |
| StartedAt: 2023-03-23 19:01:31 -0400 (Thu, 23 Mar 2023) |
| EndedAt: 2023-03-23 19:12:48 -0400 (Thu, 23 Mar 2023) |
| EllapsedTime: 676.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Biostrings.Rcheck |
| Warnings: 3 |
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### Running 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_2.67.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Biostrings.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-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 ‘2.67.0’
* 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 ... WARNING
Found the following significant warnings:
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.ptr’ is used uninitialized [-Wuninitialized]
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.length’ is used uninitialized [-Wuninitialized]
See ‘/home/biocbuild/bbs-3.17-bioc/meat/Biostrings.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 13.7Mb
sub-directories of 1Mb or more:
R 1.3Mb
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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::testPackage’ ‘IRanges:::.showAtomicList’
‘IRanges:::from_Vector_to_CompressedList’
‘IRanges:::new_CompressedList_from_list’ ‘IRanges:::new_Views’
‘IRanges:::regroupBySupergroup’ ‘IRanges:::show_IntegerRangesList’
‘IRanges:::unlist_as_integer’ ‘S4Vectors:::anyMissingOrOutside’
‘XVector:::close_filexp’
‘XVector:::extract_character_from_XRaw_by_positions’
‘XVector:::extract_character_from_XRaw_by_ranges’
‘XVector:::new_XVectorList_from_list_of_XVector’
‘XVector:::open_output_file’
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) 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 280.492 2.268 282.766
matchPDict-inexact 63.149 0.596 63.746
findPalindromes 38.276 0.100 38.378
XStringSet-class 9.016 0.412 9.430
XStringSet-io 7.887 0.244 8.133
matchPattern 5.387 0.244 5.631
* 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 ...
‘Biostrings2Classes.Rnw’ using ‘UTF-8’... OK
‘BiostringsQuickOverview.Rnw’ using ‘UTF-8’... OK
‘MultipleAlignments.Rnw’ using ‘UTF-8’... OK
‘PairwiseAlignments.Rnw’ using ‘UTF-8’... OK
‘matchprobes.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 4 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/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/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c BAB_class.c -o BAB_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function]
299 | static void BitMatrix_print(BitMatrix *bitmat)
| ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:184:27: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
184 | IntAE *poffsets, *poffsets_order;
| ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’:
XStringSet_class.c:124:17: warning: ‘lkup_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
125 | INTEGER(start)[i], lkup0, lkup_len);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XString_class.c -o XString_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:155:29: warning: ‘sc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
155 | INTEGER(ans_elt)[0] = score;
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’:
align_utils.c:250:42: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
250 | jPattern += indelWidthSubject;
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:231:63: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
231 | if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
| ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:239:72: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
239 | mappedStringPtr[index] = gapCodeValue;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
align_utils.c:232:78: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
232 | if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’:
letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable]
957 | int x_width, y_width, x_length, *ans_mat, i, x_pos;
| ^~~~~
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
956 | SEXP ans, ans_dimnames;
| ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function]
7 | static void test_match_pattern_indels(const char *p, const char *s,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:419:33: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
419 | ans_col += tb_length;
| ~~~~~~~~^~~~~~~~~~~~
match_pdict.c:392:65: note: ‘ans_col’ was declared here
392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
| ^~~~~~~
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:470:41: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
470 | ans_elt += P_length;
| ~~~~~~~~^~~~~~~~~~~
match_pdict.c:441:64: note: ‘ans_elt’ was declared here
441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function ‘split_and_move_pointers’:
match_pdict_ACtree2.c:1031:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
1031 | ACnode *node0, *node1, *node2;
| ^~~~~
match_pdict_ACtree2.c: In function ‘merge_pointers’:
match_pdict_ACtree2.c:1076:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
1076 | ACnode *node0, *node1, *node2;
| ^~~~~
At top level:
match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function]
139 | static void debug_node_counting_functions(int maxdepth)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:75:27: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
| ^~~~~~~~~~~~~~~~~~~~~
match_pdict_Twobit.c:110:19: note: ‘twobit_sign2pos’ was declared here
110 | SEXP ans, twobit_sign2pos;
| ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:653:56: warning: unused variable ‘ncol’ [-Wunused-variable]
653 | int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
| ^~~~
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:713:13: warning: unused variable ‘nelt’ [-Wunused-variable]
713 | int nelt, nkey0, nkey1, nkey2, i, key;
| ^~~~
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:820:51: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~~~~
match_pdict_utils.c:820:34: warning: unused variable ‘total_NFC’ [-Wunused-variable]
820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~
match_pdict_utils.c:819:40: warning: unused variable ‘NFC’ [-Wunused-variable]
819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
| ^~~
match_pdict_utils.c:819:33: warning: unused variable ‘nloci’ [-Wunused-variable]
819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
| ^~~~~
match_pdict_utils.c:819:27: warning: unused variable ‘ndup’ [-Wunused-variable]
819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
| ^~~~
At top level:
match_pdict_utils.c:820:34: warning: ‘total_NFC’ defined but not used [-Wunused-variable]
820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~
match_pdict_utils.c:820:51: warning: ‘subtotal_NFC’ defined but not used [-Wunused-variable]
820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~~~~
match_pdict_utils.c:261:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function]
261 | static void match_headtail_by_loc(const HeadTail *headtail,
| ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_fasta_files.c -o read_fasta_files.o
In function ‘new_FASTAloaderExt’,
inlined from ‘read_fasta_files’ at read_fasta_files.c:430:15:
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
186 | return loader_ext;
| ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_files’:
read_fasta_files.c:182:24: note: ‘loader_ext’ declared here
182 | FASTAloaderExt loader_ext;
| ^~~~~~~~~~
In function ‘new_FASTAloaderExt’,
inlined from ‘read_fasta_files’ at read_fasta_files.c:430:15:
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.length’ may be used uninitialized [-Wmaybe-uninitialized]
186 | return loader_ext;
| ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_files’:
read_fasta_files.c:182:24: note: ‘loader_ext’ declared here
182 | FASTAloaderExt loader_ext;
| ^~~~~~~~~~
In function ‘new_FASTAloaderExt’,
inlined from ‘read_fasta_blocks’ at read_fasta_files.c:596:15:
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.ptr’ is used uninitialized [-Wuninitialized]
186 | return loader_ext;
| ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_blocks’:
read_fasta_files.c:182:24: note: ‘loader_ext’ declared here
182 | FASTAloaderExt loader_ext;
| ^~~~~~~~~~
In function ‘new_FASTAloaderExt’,
inlined from ‘read_fasta_blocks’ at read_fasta_files.c:596:15:
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.length’ is used uninitialized [-Wuninitialized]
186 | return loader_ext;
| ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_blocks’:
read_fasta_files.c:182:24: note: ‘loader_ext’ declared here
182 | FASTAloaderExt loader_ext;
| ^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function ‘parse_FASTQ_file’:
read_fastq_files.c:392:28: warning: ‘dont_load’ may be used uninitialized in this function [-Wmaybe-uninitialized]
392 | if (dont_load || loader->new_empty_seq_hook == NULL)
| ^
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c translate.c -o translate.o
translate.c: In function ‘DNAStringSet_translate’:
translate.c:110:36: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
110 | if (if_ambig == TRANSLATE_ERROR) {
| ^
translate.c:136:36: note: ‘if_ambig0’ was declared here
136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
| ^~~~~~~~~
translate.c:106:36: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | if (if_non_ambig == TRANSLATE_TO_X)
| ^
translate.c:136:21: note: ‘if_non_ambig0’ was declared here
136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
| ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature’:
utils.c:157:16: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
157 | return twobit_sign;
| ^~~~~~~~~~~
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:164:19: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
164 | int i, j, twobit_sign;
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c xscat.c -o xscat.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
xscat.c: In function ‘XString_xscat’:
/home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:91:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized]
91 | #define NEW_RAW(n) Rf_allocVector(RAWSXP,n)
| ^~~~~~~~~~~~~~
xscat.c:18:20: note: ‘ans_length’ was declared here
18 | int nargs, ans_length, tag_offset, j;
| ^~~~~~~~~~
xscat.c:52:23: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized]
52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
| ^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
xscat.c: In function ‘XStringSet_xscat’:
/home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:85:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized]
85 | #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n)
| ^~~~~~~~~~~~~~
xscat.c:66:39: note: ‘ans_length’ was declared here
66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
| ^~~~~~~~~~
xscat.c:108:23: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
| ^~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -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 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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
R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu (64-bit)
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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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 -- Thu Mar 23 19:10:34 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
9.193 0.344 9.533
Biostrings.Rcheck/Biostrings-Ex.timings
| name | user | system | elapsed | |
| AAString-class | 0.003 | 0.001 | 0.004 | |
| AMINO_ACID_CODE | 0.002 | 0.000 | 0.002 | |
| AlignedXStringSet-class | 0.056 | 0.000 | 0.056 | |
| DNAString-class | 0.004 | 0.000 | 0.004 | |
| GENETIC_CODE | 0.009 | 0.003 | 0.012 | |
| HNF4alpha | 0.018 | 0.000 | 0.018 | |
| IUPAC_CODE_MAP | 0.112 | 0.015 | 0.127 | |
| MIndex-class | 0 | 0 | 0 | |
| MaskedXString-class | 0.178 | 0.023 | 0.202 | |
| MultipleAlignment-class | 0.931 | 0.056 | 0.988 | |
| PDict-class | 3.989 | 0.161 | 4.152 | |
| PairwiseAlignments-class | 0.504 | 0.017 | 0.522 | |
| PairwiseAlignments-io | 2.152 | 0.246 | 2.397 | |
| QualityScaledXStringSet-class | 0.120 | 0.004 | 0.125 | |
| RNAString-class | 0.006 | 0.000 | 0.007 | |
| XString-class | 0.007 | 0.000 | 0.007 | |
| XStringQuality-class | 0.121 | 0.000 | 0.121 | |
| XStringSet-class | 9.016 | 0.412 | 9.430 | |
| XStringSet-comparison | 3.239 | 0.200 | 3.439 | |
| XStringSet-io | 7.887 | 0.244 | 8.133 | |
| XStringSetList-class | 0.201 | 0.008 | 0.210 | |
| XStringViews-class | 0.103 | 0.012 | 0.115 | |
| align-utils | 0.027 | 0.012 | 0.038 | |
| chartr | 0.509 | 0.052 | 0.562 | |
| detail | 0.231 | 0.055 | 0.286 | |
| dinucleotideFrequencyTest | 0.012 | 0.000 | 0.012 | |
| findPalindromes | 38.276 | 0.100 | 38.378 | |
| getSeq | 0.038 | 0.020 | 0.059 | |
| gregexpr2 | 0.002 | 0.000 | 0.002 | |
| injectHardMask | 0.036 | 0.008 | 0.044 | |
| letter | 0.024 | 0.000 | 0.024 | |
| letterFrequency | 0.640 | 0.048 | 0.688 | |
| longestConsecutive | 0 | 0 | 0 | |
| lowlevel-matching | 0.331 | 0.028 | 0.359 | |
| maskMotif | 1.045 | 0.036 | 1.082 | |
| match-utils | 0.02 | 0.00 | 0.02 | |
| matchLRPatterns | 0.391 | 0.019 | 0.415 | |
| matchPDict-exact | 280.492 | 2.268 | 282.766 | |
| matchPDict-inexact | 63.149 | 0.596 | 63.746 | |
| matchPWM | 2.19 | 0.00 | 2.19 | |
| matchPattern | 5.387 | 0.244 | 5.631 | |
| matchProbePair | 1.186 | 0.004 | 1.190 | |
| matchprobes | 0.244 | 0.000 | 0.244 | |
| misc | 0.015 | 0.001 | 0.016 | |
| needwunsQS | 0 | 0 | 0 | |
| nucleotideFrequency | 0.547 | 0.041 | 0.588 | |
| padAndClip | 0.378 | 0.000 | 0.378 | |
| pairwiseAlignment | 0.637 | 0.012 | 0.649 | |
| phiX174Phage | 0.428 | 0.004 | 0.433 | |
| pid | 0.362 | 0.024 | 0.387 | |
| replaceAt | 2.117 | 0.064 | 2.181 | |
| replaceLetterAt | 0.353 | 0.072 | 0.425 | |
| reverseComplement | 0.986 | 0.008 | 0.994 | |
| seqinfo-methods | 0.497 | 0.000 | 0.497 | |
| stringDist | 3.259 | 0.000 | 3.259 | |
| substitution_matrices | 0.729 | 0.004 | 0.733 | |
| toComplex | 0.002 | 0.000 | 0.001 | |
| translate | 0.951 | 0.044 | 0.994 | |
| trimLRPatterns | 0.051 | 0.004 | 0.055 | |
| xscat | 0.926 | 0.020 | 0.946 | |
| yeastSEQCHR1 | 0.003 | 0.000 | 0.003 | |