Hervé Pagès
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/IRanges |
| git_branch: RELEASE_3_17 |
| git_last_commit: ce72113 |
| git_last_commit_date: 2023-06-21 22:44:53 -0400 (Wed, 21 Jun 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:27 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1019/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IRanges 2.34.1 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the IRanges package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IRanges.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: IRanges |
| Version: 2.34.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IRanges.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings IRanges_2.34.1.tar.gz |
| StartedAt: 2023-10-15 22:14:42 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 22:17:49 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 186.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: IRanges.Rcheck |
| Warnings: 5 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IRanges.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings IRanges_2.34.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/IRanges.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘2.34.1’
* 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 ‘IRanges’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setCompressedListSummaryMethod : <anonymous>: no visible binding for
global variable ‘C_fun’
setCompressedListWhichSummaryMethod : def: no visible binding for
global variable ‘C_fun’
Undefined global functions or variables:
C_fun
* checking Rd files ... WARNING
checkRd: (5) AtomicList-class.Rd:191-193: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:194-196: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:197-199: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:200-202: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:203-205: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:206-208: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:209-212: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:213-215: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:221-226: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:227-233: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:234-240: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:241-250: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:251-253: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:254-257: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:258-261: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:262-273: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:289-291: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:292-294: \item in \describe must have non-empty label
checkRd: (5) AtomicList-class.Rd:295-297: \item in \describe must have non-empty label
checkRd: (5) AtomicList-utils.Rd:214: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:146-147: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:148-151: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:156-157: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:158-159: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:160-166: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:167-169: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:178-186: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:187-192: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:198-199: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:200-209: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:218-221: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:222-225: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:231-235: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:242-246: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:247-253: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:254-257: \item in \describe must have non-empty label
checkRd: (5) DataFrameList-class.Rd:258-264: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:206-209: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:210-213: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:214-217: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:222-226: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:227-235: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:260-265: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:266-271: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:276-285: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:286-291: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:307-310: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:311-314: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:315-325: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:337-347: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:379-405: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:406-432: \item in \describe must have non-empty label
checkRd: (5) Grouping-class.Rd:433-440: \item in \describe must have non-empty label
checkRd: (5) Hits-class-leftovers.Rd:45-47: \item in \describe must have non-empty label
checkRd: (5) Hits-class-leftovers.Rd:48-49: \item in \describe must have non-empty label
checkRd: (5) Hits-class-leftovers.Rd:50-53: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:108-111: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:112-116: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:117-121: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:122-125: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:126-129: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:130-133: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:134-141: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:142-150: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:151-154: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:155-160: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:161-168: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:169-173: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:174-182: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:183-195: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:196-202: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:203-213: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:214-217: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:218-228: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:269-272: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-class.Rd:273-277: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:123-168: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:169-177: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:178-184: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:185-189: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:190-199: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:200-207: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:208-213: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:214-218: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:219-223: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:224-229: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:230-234: \item in \describe must have non-empty label
checkRd: (5) IPosRanges-comparison.Rd:235-239: \item in \describe must have non-empty label
checkRd: (5) IRanges-class.Rd:70-74: \item in \describe must have non-empty label
checkRd: (5) IRanges-class.Rd:75-82: \item in \describe must have non-empty label
checkRd: (5) IRanges-class.Rd:83-87: \item in \describe must have non-empty label
checkRd: (5) IRanges-class.Rd:93-99: \item in \describe must have non-empty label
checkRd: (5) IRanges-class.Rd:105-108: \item in \describe must have non-empty label
checkRd: (5) IRanges-class.Rd:109-112: \item in \describe must have non-empty label
checkRd: (5) IRanges-constructor.Rd:86-138: \item in \describe must have non-empty label
checkRd: (5) IRangesList-class.Rd:83-93: \item in \describe must have non-empty label
checkRd: (5) IRangesList-class.Rd:100-106: \item in \describe must have non-empty label
checkRd: (5) IRangesList-class.Rd:107-113: \item in \describe must have non-empty label
checkRd: (5) IRangesList-class.Rd:114-118: \item in \describe must have non-empty label
checkRd: (5) IRangesList-class.Rd:119-123: \item in \describe must have non-empty label
checkRd: (5) IRangesList-class.Rd:128-132: \item in \describe must have non-empty label
checkRd: (5) IRangesList-class.Rd:138-142: \item in \describe must have non-empty label
checkRd: (5) IRangesList-class.Rd:143-147: \item in \describe must have non-empty label
checkRd: (5) IntegerRangesList-class.Rd:87-90: \item in \describe must have non-empty label
checkRd: (5) IntegerRangesList-class.Rd:91-94: \item in \describe must have non-empty label
checkRd: (5) IntegerRangesList-class.Rd:95-98: \item in \describe must have non-empty label
checkRd: (5) IntegerRangesList-class.Rd:99-102: \item in \describe must have non-empty label
checkRd: (5) IntegerRangesList-class.Rd:109-115: \item in \describe must have non-empty label
checkRd: (5) IntegerRangesList-class.Rd:121-124: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:87-90: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:91-96: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:97-101: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:102-105: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:106-109: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:110-114: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:120-129: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:137-141: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:142-146: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:147-151: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:152-157: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:158-161: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:170-174: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:175-179: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:180-183: \item in \describe must have non-empty label
checkRd: (5) MaskCollection-class.Rd:191-195: \item in \describe must have non-empty label
checkRd: (5) RangedSelection-class.Rd:38-41: \item in \describe must have non-empty label
checkRd: (5) RangedSelection-class.Rd:47-51: \item in \describe must have non-empty label
checkRd: (5) RangedSelection-class.Rd:58-61: \item in \describe must have non-empty label
checkRd: (5) RangedSelection-class.Rd:62-64: \item in \describe must have non-empty label
checkRd: (5) Rle-class-leftovers.Rd:29-32: \item in \describe must have non-empty label
checkRd: (5) Rle-class-leftovers.Rd:33-36: \item in \describe must have non-empty label
checkRd: (5) Rle-class-leftovers.Rd:44-56: \item in \describe must have non-empty label
checkRd: (5) Rle-class-leftovers.Rd:57-61: \item in \describe must have non-empty label
checkRd: (5) Rle-class-leftovers.Rd:62-66: \item in \describe must have non-empty label
checkRd: (5) RleViewsList-class.Rd:32-38: \item in \describe must have non-empty label
checkRd: (5) RleViewsList-class.Rd:39-41: \item in \describe must have non-empty label
checkRd: (5) RleViewsList-class.Rd:49-52: \item in \describe must have non-empty label
checkRd: (5) Vector-class-leftovers.Rd:33-36: \item in \describe must have non-empty label
checkRd: (5) Vector-class-leftovers.Rd:37-43: \item in \describe must have non-empty label
checkRd: (5) Vector-class-leftovers.Rd:53-64: \item in \describe must have non-empty label
checkRd: (5) Vector-class-leftovers.Rd:72-79: \item in \describe must have non-empty label
checkRd: (5) Vector-class-leftovers.Rd:85-88: \item in \describe must have non-empty label
checkRd: (5) Views-class.Rd:55-73: \item in \describe must have non-empty label
checkRd: (5) Views-class.Rd:81-84: \item in \describe must have non-empty label
checkRd: (5) Views-class.Rd:94-97: \item in \describe must have non-empty label
checkRd: (5) Views-class.Rd:103-105: \item in \describe must have non-empty label
checkRd: (5) Views-class.Rd:106-115: \item in \describe must have non-empty label
checkRd: (5) Views-class.Rd:121-124: \item in \describe must have non-empty label
checkRd: (5) Views-class.Rd:130-135: \item in \describe must have non-empty label
checkRd: (5) Views-class.Rd:136-142: \item in \describe must have non-empty label
checkRd: (5) Views-class.Rd:143-148: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IntegerRangesList-class.Rd':
‘[IRanges]{RangesList}’
Missing link or links in documentation object 'intra-range-methods.Rd':
‘RangesList’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘%poutside%’ ‘%pover%’ ‘%pwithin%’ ‘cvg’ ‘heads’ ‘slidingIRanges’
‘slidingViews’ ‘tails’ ‘windows’
Undocumented S4 classes:
‘BaseManyToManyGrouping’ ‘Pos’ ‘CompressedIntegerRangesList’
‘IPosList’ ‘CompressedRangesList’ ‘SimpleIPosList’ ‘RangesList’
‘CompressedPosList’ ‘CompressedIPosList’ ‘Ranges’ ‘SimplePosList’
‘PosList’ ‘SimpleRangesList’
Undocumented S4 methods:
generic 'anyDuplicated' and siglist 'RangesNSBS'
generic 'as.factor' and siglist 'ManyToOneGrouping'
generic 'as.integer' and siglist 'NormalIRanges'
generic 'as.integer' and siglist 'Pos'
generic 'as.integer' and siglist 'RangesNSBS'
generic 'cbind' and siglist 'Rle'
generic 'cbind' and siglist 'RleList'
generic 'chartr' and siglist 'ANY,ANY,CharacterList'
generic 'chartr' and siglist 'ANY,ANY,RleList'
generic 'coerce' and siglist 'ANY,IPosRanges'
generic 'coerce' and siglist 'AtomicList,RleViews'
generic 'coerce' and siglist 'IPosRanges,CompressedIntegerList'
generic 'coerce' and siglist 'IPosRanges,IntegerList'
generic 'coerce' and siglist 'IRanges,IPosList'
generic 'coerce' and siglist 'IntegerRanges,CompressedIPosList'
generic 'coerce' and siglist 'IntegerRanges,IPosList'
generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
generic 'coerce' and siglist 'factor,ManyToOneGrouping'
generic 'commonColnames<-' and siglist 'SplitDataFrameList'
generic 'cvg' and siglist 'IntegerRanges'
generic 'cvg' and siglist 'IntegerRangesList'
generic 'endsWith' and siglist 'CharacterList'
generic 'endsWith' and siglist 'RleList'
generic 'extractROWS' and siglist 'CompressedList,ANY'
generic 'extractROWS' and siglist 'IPos,ANY'
generic 'extractROWS' and siglist 'MaskCollection,ANY'
generic 'extractROWS' and siglist 'NormalIRanges,ANY'
generic 'extractROWS' and siglist 'Partitioning,ANY'
generic 'extractROWS' and siglist 'Rle,RangesNSBS'
generic 'extractROWS' and siglist 'vector_OR_factor,RangesNSBS'
generic 'getListElement' and siglist 'CompressedList'
generic 'getListElement' and siglist 'CompressedNormalIRangesList'
generic 'getListElement' and siglist 'H2LGrouping'
generic 'getListElement' and siglist 'MaskCollection'
generic 'getListElement' and siglist 'NCLists'
generic 'getListElement' and siglist 'Partitioning'
generic 'getListElement' and siglist 'Views'
generic 'gsub' and siglist 'ANY,ANY,CharacterList'
generic 'gsub' and siglist 'ANY,ANY,RleList'
generic 'ifelse2' and siglist 'ANY,List,List'
generic 'is.unsorted' and siglist 'CompressedIntegerList'
generic 'is.unsorted' and siglist 'CompressedLogicalList'
generic 'is.unsorted' and siglist 'CompressedNumericList'
generic 'isNormal' and siglist 'IntegerRanges'
generic 'length' and siglist 'RangesNSBS'
generic 'nchar' and siglist 'CharacterList'
generic 'nchar' and siglist 'RleList'
generic 'pcompareRecursively' and siglist 'IPosRanges'
generic 'range' and siglist 'CompressedRleList'
generic 'relist' and siglist 'grouping,missing'
generic 'replaceROWS' and siglist 'IRanges'
generic 'replaceROWS' and siglist 'NormalIRanges'
generic 'slidingWindows' and siglist 'IntegerRanges'
generic 'startsWith' and siglist 'CharacterList'
generic 'startsWith' and siglist 'RleList'
generic 'sub' and siglist 'ANY,ANY,CharacterList'
generic 'sub' and siglist 'ANY,ANY,RleList'
generic 'tile' and siglist 'IntegerRanges'
generic 'tolower' and siglist 'CharacterList'
generic 'tolower' and siglist 'RleList'
generic 'toupper' and siglist 'CharacterList'
generic 'toupper' and siglist 'RleList'
generic 'updateObject' and siglist 'CompressedList'
generic 'updateObject' and siglist 'IPosRanges'
generic 'whichFirstNotNormal' and siglist 'IntegerRanges'
generic 'windows' and siglist 'list_OR_List'
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 ... WARNING
Documented arguments not in \usage in documentation object 'nearest-methods':
‘hits’ ‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/libs/IRanges.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
IPos-class 7.672 0.312 7.984
* 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 ...
‘IRangesOverview.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/IRanges.Rcheck/00check.log’
for details.
IRanges.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL IRanges
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘IRanges’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_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/usr/local/include -fpic -g -O2 -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_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/usr/local/include -fpic -g -O2 -Wall -c CompressedList_class.c -o CompressedList_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/usr/local/include -fpic -g -O2 -Wall -c Grouping_class.c -o Grouping_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/usr/local/include -fpic -g -O2 -Wall -c IPosRanges_comparison.c -o IPosRanges_comparison.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/usr/local/include -fpic -g -O2 -Wall -c IRanges_class.c -o IRanges_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/usr/local/include -fpic -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.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/usr/local/include -fpic -g -O2 -Wall -c NCList.c -o NCList.o
NCList.c:1173:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function]
1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
202 | static const NCList *next_top_down(const NCList *nclist)
| ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_IRanges.c -o R_init_IRanges.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/usr/local/include -fpic -g -O2 -Wall -c Ranges_class.c -o Ranges_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/usr/local/include -fpic -g -O2 -Wall -c RleViews_utils.c -o RleViews_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/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/usr/local/include -fpic -g -O2 -Wall -c SimpleIRangesList_class.c -o SimpleIRangesList_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/usr/local/include -fpic -g -O2 -Wall -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:579:35: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
579 | if (*out_ranges_are_tiles && x_end != cvg_len)
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
coverage_methods.c:495:28: note: ‘x_end’ was declared here
495 | i, j, x_start, x_end, shift_elt, tmp;
| ^~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function ‘C_find_partition_overlaps’:
extractListFragments.c:66:33: warning: ‘split_partitions_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
66 | IntAE_insert_at(split_partitions_buf,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
67 | IntAE_get_nelt(split_partitions_buf),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | q_prev_end);
| ~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c inter_range_methods.c -o inter_range_methods.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-IRanges/00new/IRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
** 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 (IRanges)
IRanges.Rcheck/tests/run_unitTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("IRanges") || stop("unable to load IRanges package")
Loading required package: IRanges
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
[1] TRUE
> IRanges:::.test()
RUNIT TEST PROTOCOL -- Sun Oct 15 22:17:19 2023
***********************************************
Number of test functions: 98
Number of errors: 0
Number of failures: 0
1 Test Suite :
IRanges RUnit Tests - 98 test functions, 0 errors, 0 failures
Number of test functions: 98
Number of errors: 0
Number of failures: 0
Warning messages:
1: In recycleListElements(e1, en) :
Some element lengths are not multiples of their corresponding element length in e1
2: In x + y :
longer object length is not a multiple of shorter object length
3: In recycleListElements(e1, en) :
Some element lengths are not multiples of their corresponding element length in e1
4: In x + y :
longer object length is not a multiple of shorter object length
>
> proc.time()
user system elapsed
79.480 0.377 79.854
IRanges.Rcheck/IRanges-Ex.timings
| name | user | system | elapsed | |
| AtomicList-class | 0.183 | 0.012 | 0.194 | |
| AtomicList-utils | 0.037 | 0.004 | 0.041 | |
| CompressedList-class | 0.029 | 0.000 | 0.029 | |
| DataFrameList-class | 0.09 | 0.00 | 0.09 | |
| Grouping-class | 0.027 | 0.019 | 0.046 | |
| Hits-class-leftovers | 0.052 | 0.004 | 0.057 | |
| IPos-class | 7.672 | 0.312 | 7.984 | |
| IPosRanges-class | 0.037 | 0.000 | 0.037 | |
| IPosRanges-comparison | 0.038 | 0.009 | 0.046 | |
| IRanges-class | 2.647 | 0.030 | 2.678 | |
| IRanges-constructor | 0.049 | 0.004 | 0.053 | |
| IRanges-utils | 2.650 | 0.023 | 2.674 | |
| IRangesList-class | 0.039 | 0.000 | 0.039 | |
| IntegerRangesList-class | 0.061 | 0.000 | 0.060 | |
| MaskCollection-class | 0.065 | 0.000 | 0.065 | |
| NCList-class | 0.02 | 0.00 | 0.02 | |
| RangedSelection-class | 0.014 | 0.004 | 0.017 | |
| Rle-class-leftovers | 0.003 | 0.000 | 0.004 | |
| RleViews-class | 0.032 | 0.008 | 0.040 | |
| RleViewsList-class | 0.039 | 0.003 | 0.042 | |
| Views-class | 0.033 | 0.004 | 0.037 | |
| ViewsList-class | 0.001 | 0.000 | 0.001 | |
| coverage-methods | 0.172 | 0.000 | 0.172 | |
| extractList | 0.053 | 0.024 | 0.076 | |
| extractListFragments | 0.569 | 0.016 | 0.585 | |
| findOverlaps-methods | 0.272 | 0.004 | 0.275 | |
| inter-range-methods | 0.588 | 0.008 | 0.596 | |
| intra-range-methods | 0.445 | 0.018 | 0.465 | |
| multisplit | 0.014 | 0.000 | 0.015 | |
| nearest-methods | 0.106 | 0.000 | 0.106 | |
| range-squeezers | 0 | 0 | 0 | |
| read.Mask | 0.027 | 0.000 | 0.026 | |
| reverse-methods | 0.049 | 0.000 | 0.048 | |
| setops-methods | 0.781 | 0.020 | 0.801 | |
| slice-methods | 0.011 | 0.000 | 0.011 | |
| view-summarization-methods | 0.010 | 0.004 | 0.015 | |