Andreas Gschwind
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/TAPseq |
| Branch: RELEASE_3_12 |
| Last Commit: ab2957a |
| Last Changed Date: 2020-10-27 11:54:09 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:33:54 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the TAPseq package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1835/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TAPseq 1.2.0 (landing page) Andreas Gschwind
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: TAPseq |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TAPseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings TAPseq_1.2.0.tar.gz |
| StartedAt: 2021-05-06 07:26:48 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:40:03 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 794.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TAPseq.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TAPseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings TAPseq_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/TAPseq.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TAPseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TAPseq' version '1.2.0'
* 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 'TAPseq' can be installed ... WARNING
Found the following significant warnings:
Warning: Following software required by TAPseq is not installed or not in PATH:
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/TAPseq.Rcheck/00install.out' for details.
* 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 ... NOTE
Warning: Following software required by TAPseq is not installed or not in PATH:
primer3_core
makeblastdb
blastn
Please install these tools before trying to use this package!
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: Following software required by TAPseq is not installed or not in PATH:
primer3_core
makeblastdb
blastn
Please install these tools before trying to use this package!
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... 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 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
selectTargetGenes 56.55 1.70 58.31
TAPseqInput 8.06 0.29 8.36
exportPrimers 6.81 0.05 6.86
truncateTxsPolyA 6.69 0.08 6.77
pickPrimers 6.20 0.03 6.23
inferPolyASites 2.56 0.14 24.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
selectTargetGenes 67.12 1.51 68.77
pickPrimers 10.30 0.08 10.39
TAPseqInput 8.25 0.08 8.34
truncateTxsPolyA 6.00 0.08 6.08
exportPrimers 5.36 0.06 5.42
inferPolyASites 4.16 0.11 28.58
* 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/TAPseq.Rcheck/00check.log'
for details.
TAPseq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/TAPseq_1.2.0.tar.gz && rm -rf TAPseq.buildbin-libdir && mkdir TAPseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TAPseq.buildbin-libdir TAPseq_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL TAPseq_1.2.0.zip && rm TAPseq_1.2.0.tar.gz TAPseq_1.2.0.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 2012k 100 2012k 0 0 22.5M 0 --:--:-- --:--:-- --:--:-- 22.8M
install for i386
* installing *source* package 'TAPseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TAPseq'
finding HTML links ... done
TAPseq html
TAPseqInput html
TsIO-class html
TsIOList-class html
accessors html
bone_marrow_genex html
checkPrimers html
check_tool_installation html
chr11_genes html
chr11_polyA_sites html
chr11_primers html
chr11_truncated_txs html
chr11_truncated_txs_seq html
createIORecord html
designPrimers html
estimateOffTargets html
exportPrimers html
getTxsSeq html
get_gt_sequences html
inferPolyASites html
parsePrimer3Output html
pickPrimers html
selectTargetGenes html
truncateTxsPolyA html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Following software required by TAPseq is not installed or not in PATH:
primer3_core
makeblastdb
blastn
Please install these tools before trying to use this package!
** testing if installed package can be loaded from final location
Warning: Following software required by TAPseq is not installed or not in PATH:
primer3_core
makeblastdb
blastn
Please install these tools before trying to use this package!
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'TAPseq' ...
** testing if installed package can be loaded
Warning: Following software required by TAPseq is not installed or not in PATH:
primer3_core
makeblastdb
blastn
Please install these tools before trying to use this package!
* MD5 sums
packaged installation of 'TAPseq' as TAPseq_1.2.0.zip
* DONE (TAPseq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'TAPseq' successfully unpacked and MD5 sums checked
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TAPseq.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.
> library(testthat)
> library(TAPseq)
TAPseq is using the following tools:
primer3_core: NA
makeblastdb: NA
blastn: NA
Warning message:
Following software required by TAPseq is not installed or not in PATH:
primer3_core
makeblastdb
blastn
Please install these tools before trying to use this package!
>
> test_check("TAPseq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 209 ]
>
> proc.time()
user system elapsed
49.93 2.73 54.32
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TAPseq.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.
> library(testthat)
> library(TAPseq)
TAPseq is using the following tools:
primer3_core: NA
makeblastdb: NA
blastn: NA
Warning message:
Following software required by TAPseq is not installed or not in PATH:
primer3_core
makeblastdb
blastn
Please install these tools before trying to use this package!
>
> test_check("TAPseq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 209 ]
>
> proc.time()
user system elapsed
61.46 1.89 64.95
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TAPseq.Rcheck/examples_i386/TAPseq-Ex.timings
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TAPseq.Rcheck/examples_x64/TAPseq-Ex.timings
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