| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-29 16:33:51 -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 GOSim package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GOSim.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 829/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GOSim 1.37.0 (landing page) Holger Froehlich
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: GOSim |
| Version: 1.37.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GOSim.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GOSim_1.37.0.tar.gz |
| StartedAt: 2023-01-29 00:12:17 -0000 (Sun, 29 Jan 2023) |
| EndedAt: 2023-01-29 00:17:25 -0000 (Sun, 29 Jan 2023) |
| EllapsedTime: 308.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GOSim.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GOSim.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GOSim_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GOSim.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 ‘GOSim/DESCRIPTION’ ... OK
* this is package ‘GOSim’ version ‘1.37.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GOSim’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Warning message:
In utils::packageDescription(basename(dir), dirname(dir)) :
no package 'GOSim' was found
* 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(GOSim, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘GOSim’
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOGraph: no visible global function definition for ‘new’
GOenrichment: no visible global function definition for ‘new’
calc.diffusion.kernel: no visible global function definition for ‘as’
evaluateClustering: no visible global function definition for ‘median’
evaluateClustering: no visible global function definition for ‘mad’
evaluateClustering: no visible global function definition for ‘as.dist’
norm: no visible global function definition for ‘dist’
pca: no visible global function definition for ‘prcomp’
selectPrototypes : <anonymous>: no visible global function definition
for ‘cutree’
selectPrototypes : <anonymous>: no visible global function definition
for ‘hclust’
selectPrototypes : <anonymous>: no visible global function definition
for ‘dist’
selectPrototypes: no visible binding for global variable ‘BIC’
setEvidenceLevel: no visible global function definition for ‘is’
Undefined global functions or variables:
BIC as as.dist cutree dist hclust is mad median new prcomp
Consider adding
importFrom("methods", "as", "is", "new")
importFrom("stats", "BIC", "as.dist", "cutree", "dist", "hclust",
"mad", "median", "prcomp")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) setEvidenceLevel.Rd:39: Escaped LaTeX specials: \$
checkRd: (-1) setEvidenceLevel.Rd:41: Escaped LaTeX specials: \$ \$
checkRd: (-1) setEvidenceLevel.Rd:43: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:46: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:49: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:52: Escaped LaTeX specials: \$ \$
checkRd: (-1) setEvidenceLevel.Rd:54: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:58: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:61: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:64: Escaped LaTeX specials: \$
checkRd: (-1) setEvidenceLevel.Rd:66: Escaped LaTeX specials: \$ \$
checkRd: (-1) setEvidenceLevel.Rd:68: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:71: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:74: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:78: Escaped LaTeX specials: \$ \$
checkRd: (-1) setEvidenceLevel.Rd:80: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:84: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) setEvidenceLevel.Rd:87: Escaped LaTeX specials: \$ \$ \$
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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 ...
‘GOSim.Rnw’ using ‘latin1’... OK
OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘GOSim.Rnw’ using Sweave
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
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: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: annotate
Loading required package: XML
initializing GOSim package ...
-> retrieving GO information for all available genes for organism 'human' in GO database
-> filtering GO terms according to evidence levels 'all'
-> loading files with information content for corresponding GO category (human)
finished.
Attaching package: ‘igraph’
The following object is masked from ‘package:IRanges’:
union
The following object is masked from ‘package:S4Vectors’:
union
The following objects are masked from ‘package:BiocGenerics’:
normalize, path, union
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: graph
Attaching package: ‘graph’
The following objects are masked from ‘package:igraph’:
degree, edges, intersection
The following object is masked from ‘package:XML’:
addNode
Loading required package: SparseM
Attaching package: ‘SparseM’
The following object is masked from ‘package:base’:
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: ‘topGO’
The following objects are masked from ‘package:igraph’:
algorithm, graph
The following object is masked from ‘package:IRanges’:
members
Building most specific GOs .....
( 1242 GO terms found. )
Build GO DAG topology ..........
( 3677 GO terms and 7971 relations. )
Annotating nodes ...............
( 250 genes annotated to the GO terms. )
-- Elim Algorithm --
the algorithm is scoring 711 nontrivial nodes
parameters:
test statistic: fisher
cutOff: 0.01
Level 16: 1 nodes to be scored (0 eliminated genes)
Level 15: 1 nodes to be scored (0 eliminated genes)
Level 14: 1 nodes to be scored (0 eliminated genes)
Level 13: 3 nodes to be scored (0 eliminated genes)
Level 12: 10 nodes to be scored (0 eliminated genes)
Level 11: 19 nodes to be scored (0 eliminated genes)
Level 10: 40 nodes to be scored (0 eliminated genes)
Level 9: 62 nodes to be scored (4 eliminated genes)
Level 8: 82 nodes to be scored (24 eliminated genes)
Level 7: 115 nodes to be scored (30 eliminated genes)
Level 6: 127 nodes to be scored (33 eliminated genes)
Level 5: 123 nodes to be scored (33 eliminated genes)
Killed
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/GOSim.Rcheck/00check.log’
for details.
GOSim.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GOSim ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘GOSim’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "require(Rcpp); Rcpp:::CxxFlags()"` -fPIC -g -O2 -Wall -c OAWrapper.cpp -o OAWrapper.o Loading required package: Rcpp gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c hungarian2.c -o hungarian2.o Loading required package: Rcpp g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o GOSim.so OAWrapper.o hungarian2.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR Loading required package: Rcpp installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-GOSim/00new/GOSim/libs ** R ** data ** 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 (GOSim)