Josef Spidlen
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/FlowRepositoryR |
| Branch: RELEASE_3_9 |
| Last Commit: e8ae547 |
| Last Changed Date: 2019-05-02 11:53:54 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:06:42 -0400 (Wed, 16 Oct 2019).
| Package 577/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FlowRepositoryR 1.16.0 Josef Spidlen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: FlowRepositoryR |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:FlowRepositoryR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings FlowRepositoryR_1.16.0.tar.gz |
| StartedAt: 2019-10-16 01:41:53 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:42:41 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 48.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowRepositoryR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:FlowRepositoryR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings FlowRepositoryR_1.16.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/FlowRepositoryR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowRepositoryR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FlowRepositoryR’ version ‘1.16.0’
* 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 ‘FlowRepositoryR’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
attachmentProxy: no visible global function definition for ‘new’
fcsProxy: no visible global function definition for ‘new’
flowRep.search: no visible global function definition for ‘is’
flowRepData: no visible global function definition for ‘new’
flowRepOrganization: no visible global function definition for ‘new’
attachments<-,flowRepData: no visible global function definition for
‘is’
fcs.files<-,flowRepData: no visible global function definition for ‘is’
impc.experiments<-,flowRepData: no visible global function definition
for ‘is’
Undefined global functions or variables:
is new
Consider adding
importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 1 NOTE
See
‘/home/biocbuild/bbs-3.9-bioc/meat/FlowRepositoryR.Rcheck/00check.log’
for details.
FlowRepositoryR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL FlowRepositoryR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘FlowRepositoryR’ ... ** using staged installation ** R ** 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 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 (FlowRepositoryR)
FlowRepositoryR.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("FlowRepositoryR")
File about.txt downloaded.
File GvHD2.fcs downloaded.
Downloading to /home/biocbuild/bbs-3.9-bioc/meat/FlowRepositoryR.Rcheck/tests/FR-FCM-ZZJ7
File GvHD2.fcs is downloaded already.
File GvHD8.fcs downloaded.
File about.txt is downloaded already.
File ExampleGate.png downloaded.
Download finished.
Loading required package: bitops
RUNIT TEST PROTOCOL -- Wed Oct 16 01:42:37 2019
***********************************************
Number of test functions: 16
Number of errors: 0
Number of failures: 0
1 Test Suite :
FlowRepositoryR RUnit Tests - 16 test functions, 0 errors, 0 failures
Number of test functions: 16
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
1.624 0.142 10.274
FlowRepositoryR.Rcheck/FlowRepositoryR-Ex.timings
| name | user | system | elapsed | |
| attachmentProxy-class | 0.157 | 0.025 | 0.592 | |
| download-methods | 0.326 | 0.056 | 1.948 | |
| fcsProxy-class | 0.093 | 0.028 | 0.382 | |
| fileProxy-class | 0.139 | 0.028 | 0.368 | |
| flowRep.get | 0.083 | 0.004 | 0.379 | |
| flowRep.ls | 0.078 | 0.008 | 0.404 | |
| flowRep.search | 0.067 | 0.000 | 2.988 | |
| flowRep.submitGeneStatus | 0.002 | 0.000 | 0.001 | |
| flowRep.submitImpcResults | 0.001 | 0.000 | 0.002 | |
| flowRepData-class | 0.083 | 0.004 | 0.264 | |
| flowRepOrganization-class | 0.087 | 0.000 | 0.328 | |
| forgetFlowRepositoryCredentials | 0.001 | 0.000 | 0.000 | |
| getFlowRepositoryURL | 0.001 | 0.000 | 0.000 | |
| id-methods | 0.111 | 0.000 | 0.453 | |
| ilarCodeDescription | 0.000 | 0.000 | 0.001 | |
| impcCodeDescription | 0.001 | 0.000 | 0.000 | |
| impcResultsCopy-methods | 0.094 | 0.011 | 0.371 | |
| is.downloaded-methods | 0.109 | 0.004 | 0.314 | |
| listKnownIlarCodes | 0.000 | 0.000 | 0.001 | |
| setFlowRepositoryCredentials | 0.000 | 0.000 | 0.001 | |
| setFlowRepositoryURL | 0.000 | 0.000 | 0.001 | |