| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-29 16:33:47 -0000 (Sun, 29 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4021 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the flagme package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flagme.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 672/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flagme 1.55.0 (landing page) Mark Robinson
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: flagme |
| Version: 1.55.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings flagme_1.55.0.tar.gz |
| StartedAt: 2023-01-28 22:59:22 -0000 (Sat, 28 Jan 2023) |
| EndedAt: 2023-01-28 23:10:49 -0000 (Sat, 28 Jan 2023) |
| EllapsedTime: 687.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flagme.Rcheck |
| Warnings: 4 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings flagme_1.55.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/flagme.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.55.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flagme’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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
* 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 loading without being on the library search path ... WARNING
Error in library(flagme, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘flagme’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘MSnbase’
Missing or unexported object: ‘xcms::rectUnique’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addXCMSPeaks: no visible global function definition for ‘bpparam’
addXCMSPeaks : <anonymous> : <anonymous>: no visible global function
definition for ‘setNames’
importSpec : <anonymous>: no visible global function definition for
‘setNames’
Undefined global functions or variables:
bpparam setNames
Consider adding
importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotAlignment-peaksAlignment-method.Rd':
‘plotAlignment’
Missing link or links in documentation object 'plotClustAlignment-clusterAlignment-method.Rd':
‘plotAlignment’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘plotAlignment’ ‘plotChrom’ ‘plotClustAlignment’
Undocumented S4 methods:
generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘flagme-knitr.Rnw’ using ‘UTF-8’... OK
‘flagme.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘flagme-knitr.Rnw’ using Sweave
Loading required package: gcspikelite
Loading required package: xcms
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
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, aperm, 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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: ProtGenerics
Attaching package: ‘ProtGenerics’
The following object is masked from ‘package:stats’:
smooth
This is MSnbase version 2.25.1
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: ‘MSnbase’
The following object is masked from ‘package:base’:
trimws
This is xcms version 3.21.0
Attaching package: ‘xcms’
The following object is masked from ‘package:stats’:
sigma
Loading required package: CAMERA
Attaching package: ‘flagme’
The following object is masked from ‘package:xcms’:
plotChrom
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Error: processing vignette 'flagme-knitr.Rnw' failed with diagnostics:
chunk 3 (label = addXCMS)
Error in reducer$value.cache[[as.character(idx)]] <- values :
wrong args for environment subassignment
--- failed re-building ‘flagme-knitr.Rnw’
--- re-building ‘flagme.Rnw’ using Sweave
Loading required package: gcspikelite
Loading required package: xcms
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
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, aperm, 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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: ProtGenerics
Attaching package: ‘ProtGenerics’
The following object is masked from ‘package:stats’:
smooth
This is MSnbase version 2.25.1
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: ‘MSnbase’
The following object is masked from ‘package:base’:
trimws
This is xcms version 3.21.0
Attaching package: ‘xcms’
The following object is masked from ‘package:stats’:
sigma
Loading required package: CAMERA
Attaching package: ‘flagme’
The following object is masked from ‘package:xcms’:
plotChrom
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Error: processing vignette 'flagme.Rnw' failed with diagnostics:
chunk 3 (label = addXCMS)
Error in reducer$value.cache[[as.character(idx)]] <- values :
wrong args for environment subassignment
--- failed re-building ‘flagme.Rnw’
SUMMARY: processing the following files failed:
‘flagme-knitr.Rnw’ ‘flagme.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/flagme.Rcheck/00check.log’
for details.
flagme.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL flagme
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c dp.c -o dp.o
dp.c: In function ‘dp’:
dp.c:263:33: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
263 | D[(i+1)+(j+1)*(nr+1)] = cur_min;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
dp.c:264:35: warning: ‘tb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
264 | phi[(i+1)+(j+1)*(nr+1)] = tb;
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-flagme/00new/flagme/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flagme)