Back to Multiple platform build/check report for BioC 3.20:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-15 13:46:29 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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

Package 378/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.41.0  (landing page)
Ge Tan
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: devel
git_last_commit: cd329da
git_last_commit_date: 2024-04-30 10:35:00 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for CNEr on kunpeng2


To the developers/maintainers of the CNEr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNEr.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: CNEr
Version: 1.40.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:CNEr.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings CNEr_1.40.0.tar.gz
StartedAt: 2024-05-09 05:59:40 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 06:11:36 -0000 (Thu, 09 May 2024)
EllapsedTime: 715.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CNEr.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:CNEr.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings CNEr_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CNEr.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNEr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNEr’ version ‘1.40.0’
* 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 ‘CNEr’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 18.5Mb
  sub-directories of 1Mb or more:
    extdata  15.9Mb
    libs      1.3Mb
* 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 code 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 ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
checkRd: (5) GRangePairs-class.Rd:58-62: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:69-72: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:73-76: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:77-85: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:86-93: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:94-98: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:99-102: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:103-106: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:115-119: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:127-133: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:141-156: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:157-160: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:161-164: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:172-175: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:176-179: \item in \describe must have non-empty label
checkRd: (5) GRangePairs-class.Rd:180-187: \item in \describe must have non-empty label
checkRd: (-1) lavToPsl.Rd:22: Lost braces
    22 |     code{character}(n): file names of output \emph{psl} files. 
       |         ^
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/CNEr/libs/CNEr.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
makeGRBs     301.861  2.924 305.259
plotCNEWidth   9.494  0.183   9.700
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/CNEr.Rcheck/00check.log’
for details.


Installation output

CNEr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL CNEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘CNEr’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c R_init_CNEr.c -o R_init_CNEr.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘bin_ranges_from_coord_range_standard’:
utils.c:50:7: warning: unused variable ‘_binNextShift’ [-Wunused-variable]
   50 |   int _binNextShift = binNextShift();
      |       ^~~~~~~~~~~~~
utils.c:49:7: warning: unused variable ‘_binFirstShift’ [-Wunused-variable]
   49 |   int _binFirstShift = binFirstShift();
      |       ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c io.c -o io.o
io.c: In function ‘myReadAxt’:
io.c:94:26: warning: unused variable ‘curAxt’ [-Wunused-variable]
   94 |   struct axt *axt=NULL, *curAxt;
      |                          ^~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ceScan.c -o ceScan.o
ceScan.c: In function ‘ceScan’:
ceScan.c:615:8: warning: unused variable ‘rest’ [-Wunused-variable]
  615 |   char rest, path[PATH_LEN];
      |        ^~~~
ceScan.c:613:10: warning: unused variable ‘n’ [-Wunused-variable]
  613 |   int i, n;
      |          ^
ceScan.c: In function ‘freeSlThreshold’:
ceScan.c:674:17: warning: unused variable ‘CNE’ [-Wunused-variable]
  674 |   struct slCNE *CNE, *nextCNE, *el_CNE;
      |                 ^~~
ceScan.c:673:23: warning: unused variable ‘thresholds’ [-Wunused-variable]
  673 |   struct slThreshold *thresholds, *nextThreshold, *el_threshold;
      |                       ^~~~~~~~~~
ceScan.c: In function ‘myCeScan’:
ceScan.c:868:28: warning: unused variable ‘i’ [-Wunused-variable]
  868 |   int nrCNE[nrThresholds], i;
      |                            ^
ceScan.c:868:7: warning: unused variable ‘nrCNE’ [-Wunused-variable]
  868 |   int nrCNE[nrThresholds], i;
      |       ^~~~~
ceScan.c:865:17: warning: unused variable ‘CNE’ [-Wunused-variable]
  865 |   struct slCNE *CNE;
      |                 ^~~
ceScan.c: In function ‘myCeScanFile’:
ceScan.c:898:7: warning: unused variable ‘nrThresholds’ [-Wunused-variable]
  898 |   int nrThresholds = GET_LENGTH(winSize);
      |       ^~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/axt.c -o ucsc/axt.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/chain.c -o ucsc/chain.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/common.c -o ucsc/common.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function ‘findHeadPolyTMaybeMask’:
ucsc/dnautil.c:942:5: warning: variable ‘pastPoly’ set but not used [-Wunused-but-set-variable]
  942 | int pastPoly = 0;
      |     ^~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=]
   30 | static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
      |                   ^~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/https.c -o ucsc/https.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/intExp.c -o ucsc/intExp.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function ‘validateOption’:
ucsc/options.c:49:11: warning: variable ‘discardMe’ set but not used [-Wunused-but-set-variable]
   49 | long long discardMe = 0;
      |           ^~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -g -fPIC  -g -O2  -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o CNEr.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lz -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-CNEr/00new/CNEr/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 (CNEr)

Tests output

CNEr.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(CNEr)

> 
> test_check("CNEr")
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 86 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_GRBs.R:1:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
 31.166   0.904  32.101 

Example timings

CNEr.Rcheck/CNEr-Ex.timings

nameusersystemelapsed
AssemblyStats0.0060.0150.147
Axt-class1.0400.0161.062
Axt-util1.1710.0201.217
CNE-class0.2450.0000.247
CNEDanRer10Hg380.0110.0000.011
CNEDensity0.8280.0000.834
GRangePairs-class0.8600.0550.917
addAncestorGO000
axisTrack0.0050.0000.005
axtChain0.0000.0000.001
axtInfo0.0010.0000.002
binner0.0030.0000.003
blatCNE0.0010.0000.000
ceScan-methods2.1110.0842.193
chainMergeSort000
chainNetSyntenic000
chainPreNet000
cneFinalListDanRer10Hg380.0300.0000.031
cneMerge0.6430.0000.645
fetchChromSizes000
fixCoordinates0.6740.0790.756
grangesPairsForDotplot0.0020.0000.002
last0.0000.0000.001
lastz000
lavToPsl000
makeAncoraFiles0.0420.0000.043
makeAxtTracks0.3260.0190.348
makeCNEDensity000
makeGRBs301.861 2.924305.259
matchDistribution0.4520.0080.461
netToAxt000
orgKEGGIds2EntrezIDs0.0000.0010.000
plotCNEDistribution0.6870.0070.696
plotCNEWidth9.4940.1839.700
psubAxt0.6360.0000.638
read.rmMask.GRanges0.0300.0040.035
read.rmskFasta0.0420.0000.043
readAncora0.1120.0000.113
readAncoraIntoSQLite1.1060.0121.120
readAxt0.0990.0000.099
readBed0.0700.0200.085
readCNERangesFromSQLite0.1210.0040.126
reverseCigar0.0020.0000.001
saveCNEToSQLite0.1530.0000.153
scoringMatrix000
subAxt-methods1.2550.0081.266
syntenicDotplot1.8610.4452.255
writeAxt0.1070.0040.112