VJ Carey
| Snapshot Date: 2018-04-12 07:35:06 -0400 (Thu, 12 Apr 2018) |
| URL: https://git.bioconductor.org/packages/cgdv17 |
| Branch: RELEASE_3_6 |
| Last Commit: e100181 |
| Last Changed Date: 2017-10-30 11:58:24 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 experimental data |
This page was generated on 2018-04-12 12:49:21 -0400 (Thu, 12 Apr 2018).
| Package 44/326 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cgdv17 0.16.0 VJ Carey
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| Package: cgdv17 |
| Version: 0.16.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cgdv17_0.16.0.tar.gz |
| StartedAt: 2018-04-12 09:46:04 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 09:49:18 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 193.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cgdv17.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cgdv17_0.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/cgdv17.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cgdv17/DESCRIPTION’ ... OK
* this is package ‘cgdv17’ version ‘0.16.0’
* 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 ‘cgdv17’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 240.1Mb
sub-directories of 1Mb or more:
data 5.6Mb
rowranges 224.9Mb
vcf 9.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to ‘org.Hs.eg.db’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘VariantAnnotation’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Missing or unexported objects:
‘IRanges::unlist’ ‘VariantAnnotation::MatrixToSnpMatrix’
Missing object imported by a ':::' call: ‘IRanges:::newCompressedList’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getRVS: warning in dir(system.file("rowranges", package = packname),
full = TRUE): partial argument match of 'full' to 'full.names'
padToReference: warning in matrix("0/0", nr = length(allv), nc =
length(lens)): partial argument match of 'nr' to 'nrow'
padToReference: warning in matrix("0/0", nr = length(allv), nc =
length(lens)): partial argument match of 'nc' to 'ncol'
padToReference : DS: no visible global function definition for
‘DNAStringSet’
padToReference: no visible global function definition for
‘elementLengths’
padToReference: no visible global function definition for
‘DNAStringSet’
upstreamToEntrez: no visible binding for global variable
‘org.Hs.egCHRLOC’
Undefined global functions or variables:
DNAStringSet elementLengths org.Hs.egCHRLOC
* checking Rd files ... NOTE
prepare_Rd: cgdv17-package.Rd:51-52: Dropping empty section \references
prepare_Rd: cgdv17-package.Rd:54-55: Dropping empty section \seealso
prepare_Rd: cgdv17-package.Rd:56-57: Dropping empty section \examples
prepare_Rd: countVariants.Rd:53-54: Dropping empty section \examples
prepare_Rd: getRVS.Rd:34-40: Dropping empty section \value
prepare_Rd: getRVS.Rd:47-49: Dropping empty section \note
prepare_Rd: getRVS.Rd:41-43: Dropping empty section \references
prepare_Rd: getRVS.Rd:53-55: Dropping empty section \seealso
prepare_Rd: getRVS.Rd:56-57: Dropping empty section \examples
prepare_Rd: padToReference.Rd:32-34: Dropping empty section \details
prepare_Rd: padToReference.Rd:35-41: Dropping empty section \value
prepare_Rd: padToReference.Rd:48-50: Dropping empty section \note
prepare_Rd: padToReference.Rd:42-44: Dropping empty section \references
prepare_Rd: padToReference.Rd:54-56: Dropping empty section \seealso
prepare_Rd: padToReference.Rd:57-58: Dropping empty section \examples
prepare_Rd: raggedVariantSet-class.Rd:41-43: Dropping empty section \note
prepare_Rd: raggedVariantSet-class.Rd:35-37: Dropping empty section \references
prepare_Rd: raggedVariantSet-class.Rd:47-50: Dropping empty section \seealso
prepare_Rd: variantGRanges.Rd:31-33: Dropping empty section \details
prepare_Rd: variantGRanges.Rd:34-40: Dropping empty section \value
prepare_Rd: variantGRanges.Rd:47-49: Dropping empty section \note
prepare_Rd: variantGRanges.Rd:41-43: Dropping empty section \references
prepare_Rd: variantGRanges.Rd:53-55: Dropping empty section \seealso
prepare_Rd: variantGRanges.Rd:56-57: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.6-data-experiment/meat/cgdv17.Rcheck/00check.log’
for details.
cgdv17.Rcheck/00install.out
* installing *source* package ‘cgdv17’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (cgdv17)
cgdv17.Rcheck/cgdv17-Ex.timings
| name | user | system | elapsed | |
| raggedVariantSet-class | 0.000 | 0.000 | 0.001 | |