Daniel Bottomly
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/plethy |
| git_branch: RELEASE_3_13 |
| git_last_commit: fa08dc1 |
| git_last_commit_date: 2021-05-19 11:58:57 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:16 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the plethy package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plethy.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1400/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| plethy 1.30.0 (landing page) Daniel Bottomly
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: plethy |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plethy.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings plethy_1.30.0.tar.gz |
| StartedAt: 2021-10-15 03:29:26 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 03:34:27 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 301.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: plethy.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plethy.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings plethy_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/plethy.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plethy/DESCRIPTION' ... OK
* this is package 'plethy' version '1.30.0'
* 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 whether package 'plethy' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'csv.to.table' 'find.break.ranges.integer' 'fix.time' 'multi.grep'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generate.sample.buxco : <anonymous> : <anonymous> : <anonymous> :
<anonymous>: no visible global function definition for 'rnorm'
make.db.package: no visible global function definition for
'packageDescription'
mvtsplot.data.frame: no visible global function definition for 'colors'
mvtsplot.data.frame: no visible global function definition for 'par'
mvtsplot.data.frame: no visible global function definition for 'layout'
mvtsplot.data.frame: no visible global function definition for
'strwidth'
mvtsplot.data.frame: no visible global function definition for 'abline'
mvtsplot.data.frame: no visible global function definition for 'mtext'
mvtsplot.data.frame: no visible global function definition for 'bxp'
mvtsplot.data.frame : <anonymous>: no visible binding for global
variable 'median'
mvtsplot.data.frame: no visible global function definition for 'lines'
mvtsplot.data.frame: no visible global function definition for 'Axis'
mvtsplot.data.frame: no visible global function definition for 'legend'
retrieveMatrix,BuxcoDB: no visible global function definition for
'terms'
tsplot,BuxcoDB: no visible binding for global variable 'Days'
tsplot,BuxcoDB: no visible binding for global variable 'Value'
tsplot,BuxcoDB: no visible binding for global variable 'Sample_Name'
Undefined global functions or variables:
Axis Days Sample_Name Value abline bxp colors layout legend lines
median mtext packageDescription par rnorm strwidth terms
Consider adding
importFrom("grDevices", "colors")
importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend",
"lines", "mtext", "par", "strwidth")
importFrom("stats", "median", "rnorm", "terms")
importFrom("utils", "packageDescription")
to your NAMESPACE file.
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
utilities 5.42 0.13 5.54
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
utilities 5.19 0.11 5.3
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/plethy.Rcheck/00check.log'
for details.
plethy.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/plethy_1.30.0.tar.gz && rm -rf plethy.buildbin-libdir && mkdir plethy.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plethy.buildbin-libdir plethy_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL plethy_1.30.0.zip && rm plethy_1.30.0.tar.gz plethy_1.30.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 860k 100 860k 0 0 1216k 0 --:--:-- --:--:-- --:--:-- 1219k
install for i386
* installing *source* package 'plethy' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'plethy'
finding HTML links ... done
BuxcoDB html
add_query_funcs html
dbImport html
parsing html
plethy html
utilities html
** 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
install for x64
* installing *source* package 'plethy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plethy' as plethy_1.30.0.zip
* DONE (plethy)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'plethy' successfully unpacked and MD5 sums checked
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plethy.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("plethy")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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
Loading required package: reshape2
Processing C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpOQLZwf\file64906431334f in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
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Processing C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpOQLZwf\file64905b661f65 in chunks of 10000
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Processing C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpOQLZwf\file64905a593590 in chunks of 10000
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Processing C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpOQLZwf\file6490792024e9 in chunks of 10000
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Processing C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpOQLZwf\file6490203166b5 in chunks of 10000
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RUNIT TEST PROTOCOL -- Fri Oct 15 03:33:08 2021
***********************************************
Number of test functions: 23
Number of errors: 0
Number of failures: 0
1 Test Suite :
plethy RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23
Number of errors: 0
Number of failures: 0
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
81.14 1.42 82.56
|
plethy.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> BiocGenerics:::testPackage("plethy")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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
Loading required package: reshape2
Processing C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpCKNVSW\filebe786d84595 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Processing breakpoint 2
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Processing C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpCKNVSW\filebe78be76a9c in chunks of 10000
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Processing C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpCKNVSW\filebe7822075bd5 in chunks of 10000
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Processing C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpCKNVSW\filebe783cae32c9 in chunks of 10000
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RUNIT TEST PROTOCOL -- Fri Oct 15 03:34:20 2021
***********************************************
Number of test functions: 23
Number of errors: 0
Number of failures: 0
1 Test Suite :
plethy RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23
Number of errors: 0
Number of failures: 0
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
70.00 1.14 71.14
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plethy.Rcheck/examples_i386/plethy-Ex.timings
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plethy.Rcheck/examples_x64/plethy-Ex.timings
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