Jared O'Connell
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BaseSpaceR |
| Branch: RELEASE_3_8 |
| Last Commit: 122b803 |
| Last Changed Date: 2018-10-30 11:41:51 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:49:58 -0400 (Tue, 16 Apr 2019).
| Package 99/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BaseSpaceR 1.26.0 Jared O'Connell
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BaseSpaceR |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BaseSpaceR_1.26.0.tar.gz |
| StartedAt: 2019-04-15 22:20:18 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:21:18 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 59.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BaseSpaceR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BaseSpaceR_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/BaseSpaceR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK
* this is package ‘BaseSpaceR’ version ‘1.26.0’
* 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 ‘BaseSpaceR’ can be installed ... OK
* 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
'library' or 'require' call to ‘Rsamtools’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
asBamFile: no visible global function definition for ‘BamFile’
GET,ServiceURI: no visible global function definition for
‘basicHeaderGatherer’
GET,ServiceURI: no visible global function definition for
‘basicTextGatherer’
GET,ServiceURI: no visible global function definition for ‘getForm’
GET,ServiceURI: no visible global function definition for ‘curlOptions’
POST,ServiceURI: no visible global function definition for
‘basicHeaderGatherer’
POST,ServiceURI: no visible global function definition for
‘basicTextGatherer’
POST,ServiceURI: no visible global function definition for
‘curlPerform’
POSTForm,ServiceURI: no visible global function definition for
‘basicHeaderGatherer’
POSTForm,ServiceURI: no visible global function definition for
‘basicTextGatherer’
POSTForm,ServiceURI: no visible global function definition for
‘postForm’
POSTForm,ServiceURI: no visible global function definition for
‘curlOptions’
getBAMs,AppResults: no visible binding for global variable
‘BamFileList’
getFiles,AppAuth : .toDisk: no visible global function definition for
‘CFILE’
getFiles,AppAuth : .toDisk: no visible global function definition for
‘curlPerform’
getFiles,AppAuth : .toMem: no visible global function definition for
‘getURLContent’
getFiles,AppAuth : .toMem: no visible binding for global variable
‘dsize’
Undefined global functions or variables:
BamFile BamFileList CFILE basicHeaderGatherer basicTextGatherer
curlOptions curlPerform dsize getForm getURLContent postForm
* checking Rd files ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Runs-class 0.244 0.004 6.736
Samples-class 0.196 0.008 5.336
Users-class 0.148 0.012 5.219
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/BaseSpaceR.Rcheck/00check.log’
for details.
BaseSpaceR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL BaseSpaceR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘BaseSpaceR’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (BaseSpaceR)
BaseSpaceR.Rcheck/BaseSpaceR-Ex.timings
| name | user | system | elapsed | |
| AppAuth-class | 0.360 | 0.040 | 1.555 | |
| AppResults-class | 0.000 | 0.000 | 0.001 | |
| AppSessionAuth | 0.004 | 0.000 | 0.000 | |
| AppSessions-class | 0.000 | 0.000 | 0.001 | |
| Coverage | 0.016 | 0.000 | 0.014 | |
| Error | 0.000 | 0.000 | 0.001 | |
| Files-class | 0.148 | 0.012 | 3.604 | |
| FilesExtra | 0.144 | 0.028 | 0.994 | |
| Genomes-class | 0.172 | 0.024 | 1.738 | |
| Projects-class | 0.240 | 0.028 | 2.989 | |
| Response-class | 0.004 | 0.000 | 0.002 | |
| Runs-class | 0.244 | 0.004 | 6.736 | |
| Samples-class | 0.196 | 0.008 | 5.336 | |
| ServiceURI-class | 0.000 | 0.000 | 0.001 | |
| Users-class | 0.148 | 0.012 | 5.219 | |
| Variants | 0.120 | 0.020 | 4.298 | |
| data-aAuth | 0.108 | 0.004 | 0.768 | |