James Collins
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/LOBSTAHS |
| Branch: RELEASE_3_10 |
| Last Commit: e6adc05 |
| Last Changed Date: 2019-10-29 13:09:52 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:26:56 -0400 (Wed, 15 Apr 2020).
| Package 914/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| LOBSTAHS 1.12.0 James Collins
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: LOBSTAHS |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LOBSTAHS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings LOBSTAHS_1.12.0.tar.gz |
| StartedAt: 2020-04-15 04:19:38 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:24:18 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 280.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: LOBSTAHS.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LOBSTAHS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings LOBSTAHS_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/LOBSTAHS.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LOBSTAHS/DESCRIPTION' ... OK
* this is package 'LOBSTAHS' version '1.12.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'LOBSTAHS' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMHdWr7/R.INSTALL62075626c2b/LOBSTAHS/man/doLOBscreen.Rd:20: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMHdWr7/R.INSTALL62075626c2b/LOBSTAHS/man/doLOBscreen.Rd:41: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMHdWr7/R.INSTALL62075626c2b/LOBSTAHS/man/doLOBscreen.Rd:125: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
Warning: multiple methods tables found for 'polarity<-'
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/LOBSTAHS.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: multiple methods tables found for 'polarity<-'
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: multiple methods tables found for 'polarity<-'
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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
default.LOBdbase.RData 2.0Mb 619Kb xz
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
loadLOBdbase 16.84 0.04 16.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
loadLOBdbase 9.84 0.17 10.02
* 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 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/LOBSTAHS.Rcheck/00check.log'
for details.
LOBSTAHS.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/LOBSTAHS_1.12.0.tar.gz && rm -rf LOBSTAHS.buildbin-libdir && mkdir LOBSTAHS.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LOBSTAHS.buildbin-libdir LOBSTAHS_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL LOBSTAHS_1.12.0.zip && rm LOBSTAHS_1.12.0.tar.gz LOBSTAHS_1.12.0.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 2702k 100 2702k 0 0 4763k 0 --:--:-- --:--:-- --:--:-- 4792k
install for i386
* installing *source* package 'LOBSTAHS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
Creating a new generic function for 'polarity<-' in package 'LOBSTAHS'
** help
*** installing help indices
converting help for package 'LOBSTAHS'
finding HTML links ... done
LOBSet-class html
finding level-2 HTML links ... done
LOBSet html
LOBdbase-class html
LOBdbase html
LOBdefaults html
doLOBscreen html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMHdWr7/R.INSTALL62075626c2b/LOBSTAHS/man/doLOBscreen.Rd:20: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMHdWr7/R.INSTALL62075626c2b/LOBSTAHS/man/doLOBscreen.Rd:41: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMHdWr7/R.INSTALL62075626c2b/LOBSTAHS/man/doLOBscreen.Rd:125: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
exportDBtoCSV html
extractLOBdbasedata html
generateLOBdbase html
getLOBpeaklist html
loadLOBdbase html
** building package indices
** installing vignettes
'LOBSTAHS.Rmd' using 'UTF-8'
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
Warning: multiple methods tables found for 'polarity<-'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
Warning: multiple methods tables found for 'polarity<-'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'LOBSTAHS' ...
** testing if installed package can be loaded
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
Warning: multiple methods tables found for 'polarity<-'
* MD5 sums
packaged installation of 'LOBSTAHS' as LOBSTAHS_1.12.0.zip
* DONE (LOBSTAHS)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'LOBSTAHS' successfully unpacked and MD5 sums checked
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LOBSTAHS.Rcheck/examples_i386/LOBSTAHS-Ex.timings
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LOBSTAHS.Rcheck/examples_x64/LOBSTAHS-Ex.timings
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