Nils Kurzawa
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/TPP2D |
| git_branch: RELEASE_3_13 |
| git_last_commit: 432c4fa |
| git_last_commit_date: 2021-05-19 12:43:43 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the TPP2D package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TPP2D.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 1940/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TPP2D 1.8.0 (landing page) Nils Kurzawa
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: TPP2D |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TPP2D.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TPP2D_1.8.0.tar.gz |
| StartedAt: 2021-10-15 06:48:30 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 06:51:59 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 208.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TPP2D.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TPP2D.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TPP2D_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TPP2D.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 'TPP2D/DESCRIPTION' ... OK
* this is package 'TPP2D' version '1.8.0'
* 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 'TPP2D' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plot2dTppFit':
plot2dTppFit
Code: function(df, name, model_type = "H0", optim_fun = .min_RSS_h0,
optim_fun_2 = NULL, maxit = 500, xlab =
"-log10(conc.)", ylab = "log2(summed intensities)",
dot_size = 1, line_type = "solid", fit_color =
"gray30")
Docs: function(df, name, model_type = "H0", optim_fun = .min_RSS_h0,
optim_fun_2 = NULL, maxit = 500, xlab =
"-log10(conc.)", ylab = "log2(summed intensities)",
dot_size = 0.5, line_type = "dashed", fit_color =
"darkgray")
Mismatches in argument default values:
Name: 'dot_size' Code: 1 Docs: 0.5
Name: 'line_type' Code: "solid" Docs: "dashed"
Name: 'fit_color' Code: "gray30" Docs: "darkgray"
* 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 R/sysdata.rda ... 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
computeFStatFromParams 6.65 0.01 6.67
getModelParamsDf 6.56 0.00 6.56
fitAndEvalDataset 6.05 0.00 6.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getModelParamsDf 7.50 0.00 7.52
computeFStatFromParams 7.05 0.00 7.05
fitAndEvalDataset 6.18 0.02 6.21
computeFstat 5.04 0.01 5.06
findHits 1.55 0.00 5.01
getFDR 1.45 0.00 6.84
getPvalues 0.80 0.00 5.13
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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 WARNING
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/TPP2D.Rcheck/00check.log'
for details.
TPP2D.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/TPP2D_1.8.0.tar.gz && rm -rf TPP2D.buildbin-libdir && mkdir TPP2D.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TPP2D.buildbin-libdir TPP2D_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TPP2D_1.8.0.zip && rm TPP2D_1.8.0.tar.gz TPP2D_1.8.0.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
7 1288k 7 101k 0 0 528k 0 0:00:02 --:--:-- 0:00:02 528k
99 1288k 99 1287k 0 0 1098k 0 0:00:01 0:00:01 --:--:-- 1098k
100 1288k 100 1288k 0 0 1098k 0 0:00:01 0:00:01 --:--:-- 1099k
install for i386
* installing *source* package 'TPP2D' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TPP2D'
finding HTML links ... done
TPP2D-defunct html
TPP_importCheckConfigTable html
annotateDataList html
bootstrapNull html
bootstrapNullAlternativeModel html
competeModels html
computeFStatFromParams html
computeFdr-defunct html
computeFstat html
configWide2Long html
config_tab html
filterOutContaminants html
findHits html
fitAndEvalDataset html
fitH0Model html
fitH1Model html
getFDR html
getModelParamsDf html
getPEC504Temperature html
getPvalues html
gg_qq html
import2dDataset html
import2dMain html
plot2dTppFcHeatmap html
plot2dTppFit html
plot2dTppProfile html
plot2dTppRelProfile html
plot2dTppVolcano html
raw_dat_list html
recomputeSignalFromRatios html
renameColumns html
resolveAmbiguousProteinNames html
runTPP2D html
simulated_cell_extract_df html
tpp2dExperiment-class 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 'TPP2D' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TPP2D' as TPP2D_1.8.0.zip
* DONE (TPP2D)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'TPP2D' successfully unpacked and MD5 sums checked
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TPP2D.Rcheck/tests_i386/testthat.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.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(TPP2D)
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> test_check("TPP2D")
[1] "Warning: You have specificed B < 20, it is recommended to use at least B = 20 in order to obtain reliable results."
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| | 0%
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|======================================================================| 100%
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> proc.time()
user system elapsed
6.57 0.14 6.68
|
TPP2D.Rcheck/tests_x64/testthat.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.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(TPP2D)
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> test_check("TPP2D")
[1] "Warning: You have specificed B < 20, it is recommended to use at least B = 20 in order to obtain reliable results."
|
| | 0%
|
|======================================================================| 100%
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> proc.time()
user system elapsed
7.34 0.17 7.50
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TPP2D.Rcheck/examples_i386/TPP2D-Ex.timings
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TPP2D.Rcheck/examples_x64/TPP2D-Ex.timings
|