| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:48 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 S4Vectors package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1740/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| S4Vectors 0.37.3 (landing page) Hervé Pagès
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: S4Vectors |
| Version: 0.37.3 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:S4Vectors.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings S4Vectors_0.37.3.tar.gz |
| StartedAt: 2022-12-29 03:09:39 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 03:11:07 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 87.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: S4Vectors.Rcheck |
| Warnings: 4 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:S4Vectors.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings S4Vectors_0.37.3.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/S4Vectors.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'S4Vectors/DESCRIPTION' ... OK
* this is package 'S4Vectors' version '0.37.3'
* 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 whether package 'S4Vectors' can be installed ... WARNING
Found the following significant warnings:
AEbufs.c:626:50: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
character_utils.c:187:9: warning: 'timezone' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/S4Vectors.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'data.table:::as.data.frame.data.table'
'stats:::na.exclude.data.frame' 'stats:::na.omit.data.frame'
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 ... NOTE
evalSeparately,FilterRules : <anonymous>: no visible global function
definition for '.'
Undefined global functions or variables:
.
* checking Rd files ... WARNING
checkRd: (5) Annotated-class.Rd:27-29: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:110-131: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:132-138: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:145-148: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:149-153: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:159-169: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:170-172: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:173-183: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:184-186: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:187-189: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:190-198: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:205-210: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:211-213: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:214-218: \item in \describe must have non-empty label
checkRd: (5) DataFrame-class.Rd:219-222: \item in \describe must have non-empty label
checkRd: (5) DataFrame-combine.Rd:27-36: \item in \describe must have non-empty label
checkRd: (5) DataFrame-combine.Rd:37-46: \item in \describe must have non-empty label
checkRd: (5) DataFrame-combine.Rd:47-53: \item in \describe must have non-empty label
checkRd: (5) DataFrame-combine.Rd:54-60: \item in \describe must have non-empty label
checkRd: (5) DataFrame-combine.Rd:61-65: \item in \describe must have non-empty label
checkRd: (5) DataFrame-combine.Rd:66-71: \item in \describe must have non-empty label
checkRd: (5) DataFrame-utils.Rd:27-31: \item in \describe must have non-empty label
checkRd: (5) DataFrame-utils.Rd:38-43: \item in \describe must have non-empty label
checkRd: (5) DataFrame-utils.Rd:50-53: \item in \describe must have non-empty label
checkRd: (5) DataFrame-utils.Rd:54-58: \item in \describe must have non-empty label
checkRd: (5) DataFrame-utils.Rd:59-62: \item in \describe must have non-empty label
checkRd: (5) DataFrame-utils.Rd:63-66: \item in \describe must have non-empty label
checkRd: (5) DataFrame-utils.Rd:73-76: \item in \describe must have non-empty label
checkRd: (5) DataFrame-utils.Rd:85-89: \item in \describe must have non-empty label
checkRd: (5) FilterMatrix-class.Rd:37-39: \item in \describe must have non-empty label
checkRd: (5) FilterMatrix-class.Rd:45-50: \item in \describe must have non-empty label
checkRd: (5) FilterMatrix-class.Rd:56-64: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:82-86: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:88-93: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:99-116: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:124-127: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:128-131: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:132-136: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:144-146: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:147-149: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:150-153: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:159-170: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:171-183: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:184-189: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:190-194: \item in \describe must have non-empty label
checkRd: (5) FilterRules-class.Rd:205-210: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:136: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:137: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:138: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:139: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:140: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:141-143: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:144-146: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:151: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:152: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:153: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:154: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:155: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:156: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:163-167: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:168-170: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:171-173: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:174-176: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:183-186: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:187-191: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:192-195: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:204-210: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:217-221: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:222-259: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:260-268: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:284-287: \item in \describe must have non-empty label
checkRd: (5) Hits-class.Rd:288-293: \item in \describe must have non-empty label
checkRd: (5) Hits-comparison.Rd:78-87: \item in \describe must have non-empty label
checkRd: (5) Hits-comparison.Rd:88-93: \item in \describe must have non-empty label
checkRd: (5) Hits-comparison.Rd:94-99: \item in \describe must have non-empty label
checkRd: (5) HitsList-class.Rd:69-71: \item in \describe must have non-empty label
checkRd: (5) HitsList-class.Rd:72-74: \item in \describe must have non-empty label
checkRd: (5) HitsList-class.Rd:75-78: \item in \describe must have non-empty label
checkRd: (5) HitsList-class.Rd:86-90: \item in \describe must have non-empty label
checkRd: (5) HitsList-class.Rd:91-95: \item in \describe must have non-empty label
checkRd: (5) HitsList-class.Rd:96-97: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:130-133: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:134-137: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:138-142: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:143-147: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:148-152: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:153-157: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:164-178: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:183-186: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:187-191: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:192-214: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:222-233: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:234-237: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:238-242: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:243-246: \item in \describe must have non-empty label
checkRd: (5) List-class.Rd:247-251: \item in \describe must have non-empty label
checkRd: (5) Pairs-class.Rd:57-67: \item in \describe must have non-empty label
checkRd: (5) Pairs-class.Rd:74-75: \item in \describe must have non-empty label
checkRd: (5) Pairs-class.Rd:76-77: \item in \describe must have non-empty label
checkRd: (5) Pairs-class.Rd:78-79: \item in \describe must have non-empty label
checkRd: (5) Pairs-class.Rd:85-88: \item in \describe must have non-empty label
checkRd: (5) Pairs-class.Rd:89-93: \item in \describe must have non-empty label
checkRd: (5) Pairs-class.Rd:100: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:78-82: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:83-87: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:88-92: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:93-97: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:98-101: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:108-128: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:129-135: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:136-142: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:143-152: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:160-163: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:164-167: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:168-182: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:183-207: \item in \describe must have non-empty label
checkRd: (5) RectangularData-class.Rd:208-230: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:112-120: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:128-131: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:132-135: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:136-139: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:140-143: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:144-147: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:148-151: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:159-163: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:164-168: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:176-180: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:186-192: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:193-196: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:197-201: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:202-207: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:216-224: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:225-230: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:231-235: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:236-242: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:243-251: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:252-256: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:257-262: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:263-266: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:267-270: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:271-278: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:279-282: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:283-294: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:295-307: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:308-311: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:312-315: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:316-321: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:322-332: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:333-337: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:338-344: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:345-348: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:349-354: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:355-360: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:368-371: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:372-375: \item in \describe must have non-empty label
checkRd: (5) Rle-class.Rd:376-379: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:94-99: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:107-110: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:111-115: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:123-131: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:132-136: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:137-141: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:142-145: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:146-150: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:151-155: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:156-165: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:166-170: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:171-175: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:176-190: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:191-202: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:203-210: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:211-219: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:227-236: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:237-242: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:243-252: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:253-257: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:258-262: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:263-269: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:270-276: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:277-281: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:289-292: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:293-296: \item in \describe must have non-empty label
checkRd: (5) Rle-utils.Rd:297-300: \item in \describe must have non-empty label
checkRd: (5) SimpleList-class.Rd:51-53: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:139-142: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:143-151: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:152-157: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:158-161: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:162-169: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:170-172: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:173-176: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:177-185: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:186-192: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:198-204: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:205-208: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:216-222: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:223-235: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:236-239: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:247-252: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:253-269: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:270-276: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:277-283: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:284-288: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:289-301: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:309-339: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:340-345: \item in \describe must have non-empty label
checkRd: (5) Vector-class.Rd:346-350: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'Vector-comparison.Rd':
'[IRanges]{IntegerRanges-comparison}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'I' 'head.LLint' 'pcompareRecursively' 'sort.List' 't.HitsList'
'tail.LLint' 'unname' 'window.LLint'
Undocumented S4 methods:
generic '!' and siglist 'List'
generic '<=' and siglist 'List,List'
generic '<=' and siglist 'List,list'
generic '<=' and siglist 'list,List'
generic '==' and siglist 'List,List'
generic '==' and siglist 'List,list'
generic '==' and siglist 'list,List'
generic '[' and siglist 'LLint'
generic '[<-' and siglist 'Rle'
generic 'anyNA' and siglist 'List'
generic 'by' and siglist 'Vector'
generic 'countMatches' and siglist 'ANY'
generic 'do.call' and siglist 'ANY,List'
generic 'duplicated' and siglist 'List'
generic 'eval' and siglist 'expression,Vector'
generic 'eval' and siglist 'language,Vector'
generic 'extractROWS' and siglist 'LLint,ANY'
generic 'extractROWS' and siglist 'LLint,NSBS'
generic 'extractROWS' and siglist 'LLint,RangeNSBS'
generic 'extractROWS' and siglist 'Vector,ANY'
generic 'filterRules' and siglist 'FilterResults'
generic 'from' and siglist 'HitsList'
generic 'getListElement' and siglist 'SimpleList'
generic 'grep' and siglist 'ANY,Rle'
generic 'grepl' and siglist 'ANY,Rle'
generic 'head' and siglist 'LLint'
generic 'is.na' and siglist 'List'
generic 'is.unsorted' and siglist 'List'
generic 'match' and siglist 'List,List'
generic 'match' and siglist 'List,Vector'
generic 'match' and siglist 'List,list'
generic 'match' and siglist 'List,vector'
generic 'match' and siglist 'list,List'
generic 'max' and siglist 'NSBS'
generic 'mergeROWS' and siglist 'ANY'
generic 'mergeROWS' and siglist 'Vector'
generic 'normalizeSingleBracketReplacementValue' and siglist
'DataFrame'
generic 'normalizeSingleBracketReplacementValue' and siglist 'List'
generic 'order' and siglist 'List'
generic 'pcompare' and siglist 'List,List'
generic 'pcompare' and siglist 'List,list'
generic 'pcompare' and siglist 'list,List'
generic 'pcompareRecursively' and siglist 'List'
generic 'pcompareRecursively' and siglist 'list'
generic 'rank' and siglist 'List'
generic 'rep.int' and siglist 'LLint'
generic 'replaceROWS' and siglist 'ANY'
generic 'replaceROWS' and siglist 'Rle'
generic 'replaceROWS' and siglist 'Vector'
generic 'sameAsPreviousROW' and siglist 'Rle'
generic 'sameAsPreviousROW' and siglist 'atomic'
generic 'sameAsPreviousROW' and siglist 'complex'
generic 'sameAsPreviousROW' and siglist 'integer'
generic 'sameAsPreviousROW' and siglist 'numeric'
generic 'sort' and siglist 'List'
generic 'splitAsList' and siglist 'ANY'
generic 'splitAsList' and siglist 'SortedByQueryHits'
generic 'summary' and siglist 'FilterResults'
generic 't' and siglist 'Pairs'
generic 'tail' and siglist 'LLint'
generic 'to' and siglist 'HitsList'
generic 'unique' and siglist 'List'
generic 'unique' and siglist 'SimpleList'
generic 'window' and siglist 'LLint'
generic 'with' and siglist 'Vector'
generic 'xtabs' and siglist 'Vector'
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/libs/x64/S4Vectors.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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 sizes of PDF files under 'inst/doc' ... NOTE
'qpdf' made some significant size reductions:
compacted 'S4QuickOverview.pdf' from 322Kb to 188Kb
consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
shiftApply-methods 12.75 0.52 13.26
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'run_unitTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 4 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/S4Vectors.Rcheck/00check.log'
for details.
S4Vectors.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL S4Vectors
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'S4Vectors' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AEbufs.c -o AEbufs.o
AEbufs.c: In function '_IntAEAE_toEnvir':
AEbufs.c:626:50: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
626 | snprintf(key, sizeof(key), "%010lu", i + keyshift);
| ~~~~~^ ~~~~~~~~~~~~
| | |
| | size_t {aka long long unsigned int}
| long unsigned int
| %010llu
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DataFrame_class.c -o DataFrame_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Hits_class.c -o Hits_class.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41,
from ../inst/include/S4Vectors_defines.h:18,
from S4Vectors.h:1,
from Hits_class.c:4:
F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h: In function 'Hits_new':
F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:889:33: warning: 'revmap' may be used uninitialized [-Wmaybe-uninitialized]
889 | #define defineVar Rf_defineVar
| ^~~~~~~~~~~~
Hits_class.c:216:19: note: 'revmap' was declared here
216 | SEXP ans, revmap, symbol;
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LLint_class.c -o LLint_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c List_class.c -o List_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'fill_integer_runs':
Rle_class.c:278:38: warning: 'val_out' may be used uninitialized [-Wmaybe-uninitialized]
278 | values_out[nrun_out] = val_out;
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
Rle_class.c:245:21: note: 'val_out' was declared here
245 | int val_in, val_out;
| ^~~~~~~
In function 'fill_numeric_runs',
inlined from '_construct_numeric_Rle' at Rle_class.c:765:2:
Rle_class.c:377:38: warning: 'val_out' may be used uninitialized [-Wmaybe-uninitialized]
377 | values_out[nrun_out] = val_out;
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
Rle_class.c: In function '_construct_numeric_Rle':
Rle_class.c:344:24: note: 'val_out' was declared here
344 | double val_in, val_out;
| ^~~~~~~
In function 'fill_character_runs',
inlined from '_construct_character_Rle' at Rle_class.c:813:2:
Rle_class.c:575:17: warning: 'val_out' may be used uninitialized [-Wmaybe-uninitialized]
575 | SET_STRING_ELT(values_out, nrun_out, val_out);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Rle_class.c: In function '_construct_character_Rle':
Rle_class.c:541:22: note: 'val_out' was declared here
541 | SEXP val_in, val_out;
| ^~~~~~~
In function 'fill_raw_runs',
inlined from '_construct_raw_Rle' at Rle_class.c:838:2:
Rle_class.c:671:38: warning: 'val_out' may be used uninitialized [-Wmaybe-uninitialized]
671 | values_out[nrun_out] = val_out;
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
Rle_class.c: In function '_construct_raw_Rle':
Rle_class.c:638:23: note: 'val_out' was declared here
638 | Rbyte val_in, val_out;
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rle_utils.c -o Rle_utils.o
Rle_utils.c: In function 'Rle_real_runq':
Rle_utils.c:701:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
701 | if (count_na != 0)
| ^~
Rle_utils.c:703:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
703 | q_index = roundingScale(window_len_na,
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SEXP_utils.c -o SEXP_utils.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SimpleList_class.c -o SimpleList_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c character_utils.c -o character_utils.o
character_utils.c: In function 'get_svn_time':
character_utils.c:187:9: warning: 'timezone' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
187 | utc_offset = - (timezone / 3600);
| ^~~~~~~~~~
In file included from character_utils.c:12:
c:\rtools43\x86_64-w64-mingw32.static.posix\include\time.h:276:23: note: declared here
276 | _CRTIMP extern long timezone __MINGW_ATTRIB_DEPRECATED_UCRT;
| ^~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c eval_utils.c -o eval_utils.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hash_utils.c -o hash_utils.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c integer_utils.c -o integer_utils.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c logical_utils.c -o logical_utils.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c raw_utils.c -o raw_utils.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c safe_arithm.c -o safe_arithm.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: 'sort_uchar_array' defined but not used [-Wunused-function]
263 | static void sort_uchar_array(unsigned char *x, int nelt, int desc)
| ^~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c subsetting_utils.c -o subsetting_utils.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vector_utils.c -o vector_utils.o
gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-S4Vectors/00new/S4Vectors/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'normalizeSingleBracketReplacementValue' with signature '"List"': no definition for class "List"
Creating a new generic function for 'unname' in package 'S4Vectors'
Creating a new generic function for 'expand.grid' in package 'S4Vectors'
Creating a new generic function for 'findMatches' in package 'S4Vectors'
Creating a generic function for 'setequal' from package 'base' in package 'S4Vectors'
in method for 'coerce' with signature '"Hits","DFrame"': no definition for class "DFrame"
Creating a generic function for 'as.factor' from package 'base' in package 'S4Vectors'
Creating a generic function for 'tabulate' from package 'base' in package 'S4Vectors'
Creating a generic function for 'cov' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'cor' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'runmed' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a generic function for 'substr' from package 'base' in package 'S4Vectors'
Creating a generic function for 'substring' from package 'base' in package 'S4Vectors'
Creating a generic function for 'chartr' from package 'base' in package 'S4Vectors'
Creating a generic function for 'tolower' from package 'base' in package 'S4Vectors'
Creating a generic function for 'toupper' from package 'base' in package 'S4Vectors'
Creating a generic function for 'sub' from package 'base' in package 'S4Vectors'
Creating a generic function for 'gsub' from package 'base' in package 'S4Vectors'
Creating a generic function for 'nlevels' from package 'base' in package 'S4Vectors'
in method for 'coerce' with signature '"data.table","DFrame"': no definition for class "data.table"
Creating a generic function for 'complete.cases' from package 'stats' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (S4Vectors)
S4Vectors.Rcheck/tests/run_unitTests.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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("S4Vectors") || stop("unable to load S4Vectors package")
Loading required package: S4Vectors
Loading required package: stats4
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
[1] TRUE
> S4Vectors:::.test()
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
RUNIT TEST PROTOCOL -- Thu Dec 29 03:10:54 2022
***********************************************
Number of test functions: 74
Number of errors: 0
Number of failures: 0
1 Test Suite :
S4Vectors RUnit Tests - 74 test functions, 0 errors, 0 failures
Number of test functions: 74
Number of errors: 0
Number of failures: 0
Warning messages:
1: In combineUniqueCols(X, Y, Z, use.names = FALSE) :
different values in multiple instances of column 'dup', ignoring this
column in DFrame 2
2: In combineUniqueCols(X, Y, Z) :
different values for shared rows in multiple instances of column 'dup',
ignoring this column in DFrame 2
3: In combineUniqueCols(x, y2) :
different values for shared rows in multiple instances of column 'X',
ignoring this column in DFrame 2
>
> proc.time()
user system elapsed
7.26 0.32 7.54
S4Vectors.Rcheck/S4Vectors-Ex.timings
| name | user | system | elapsed | |
| Annotated-class | 0.51 | 0.04 | 0.56 | |
| DataFrame-class | 0.16 | 0.00 | 0.15 | |
| DataFrame-combine | 0.23 | 0.00 | 0.24 | |
| DataFrame-comparison | 0.05 | 0.00 | 0.04 | |
| DataFrame-utils | 0.12 | 0.00 | 0.13 | |
| DataFrameFactor-class | 0.03 | 0.00 | 0.03 | |
| Factor-class | 0.13 | 0.00 | 0.12 | |
| FilterRules-class | 0.08 | 0.00 | 0.08 | |
| Hits-class | 0.03 | 0.00 | 0.03 | |
| Hits-comparison | 0.02 | 0.00 | 0.01 | |
| Hits-setops | 0.06 | 0.00 | 0.07 | |
| HitsList-class | 0.05 | 0.00 | 0.04 | |
| LLint-class | 0.01 | 0.00 | 0.02 | |
| List-class | 0.33 | 0.00 | 0.32 | |
| List-utils | 0.06 | 0.00 | 0.07 | |
| Pairs-class | 0.04 | 0.00 | 0.03 | |
| RectangularData-class | 0 | 0 | 0 | |
| Rle-class | 0.03 | 0.00 | 0.03 | |
| Rle-runstat | 0.11 | 0.00 | 0.11 | |
| Rle-utils | 0 | 0 | 0 | |
| SimpleList-class | 0.03 | 0.00 | 0.03 | |
| TransposedDataFrame-class | 3.08 | 0.17 | 3.25 | |
| Vector-class | 0 | 0 | 0 | |
| Vector-comparison | 0.01 | 0.03 | 0.05 | |
| Vector-merge | 0.42 | 0.05 | 0.47 | |
| Vector-setops | 0 | 0 | 0 | |
| aggregate-methods | 0.08 | 0.00 | 0.07 | |
| character-utils | 0 | 0 | 0 | |
| expand-methods | 0.27 | 0.01 | 0.29 | |
| integer-utils | 0 | 0 | 0 | |
| isSorted | 0 | 0 | 0 | |
| shiftApply-methods | 12.75 | 0.52 | 13.26 | |
| splitAsList | 0.06 | 0.00 | 0.06 | |
| stack-methods | 0.03 | 0.00 | 0.03 | |
| zip-methods | 0.02 | 0.00 | 0.02 | |