Andreas Gschwind
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/TAPseq |
| Branch: RELEASE_3_11 |
| Last Commit: 8a16f63 |
| Last Changed Date: 2020-04-27 15:34:33 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:55 -0400 (Sat, 17 Oct 2020).
| 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 1777/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TAPseq 1.0.0 Andreas Gschwind
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: TAPseq |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TAPseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TAPseq_1.0.0.tar.gz |
| StartedAt: 2020-10-17 08:47:14 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 09:01:32 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 858.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TAPseq.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TAPseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TAPseq_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TAPseq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.0.0'
* 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-3.11-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 47.44 1.43 63.60
pickPrimers 5.86 0.05 5.90
truncateTxsPolyA 5.70 0.10 5.79
TAPseqInput 5.35 0.38 5.72
inferPolyASites 2.50 0.12 25.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
selectTargetGenes 42.83 1.28 60.44
truncateTxsPolyA 8.27 0.14 8.40
pickPrimers 6.80 0.08 6.87
TAPseqInput 6.05 0.08 6.13
inferPolyASites 3.65 0.10 26.61
* 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-3.11-bioc/meat/TAPseq.Rcheck/00check.log'
for details.
TAPseq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TAPseq_1.0.0.tar.gz && rm -rf TAPseq.buildbin-libdir && mkdir TAPseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TAPseq.buildbin-libdir TAPseq_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TAPseq_1.0.0.zip && rm TAPseq_1.0.0.tar.gz TAPseq_1.0.0.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 2015k 100 2015k 0 0 17.1M 0 --:--:-- --:--:-- --:--:-- 18.2M
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_1.0.0.zip
* DONE (TAPseq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TAPseq' successfully unpacked and MD5 sums checked
|
TAPseq.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results ===========================================================
[ OK: 209 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
53.39 2.82 59.40
|
TAPseq.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results ===========================================================
[ OK: 209 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
71.48 1.89 76.62
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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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