Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-11 11:05:10 -0400 (Thu, 11 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4165
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

CHECK results for CNEr on nebbiolo2


To the developers/maintainers of the CNEr package:
- Please 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 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.

raw results

Package 354/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.33.0  (landing page)
Ge Tan
Snapshot Date: 2022-08-10 14:00:02 -0400 (Wed, 10 Aug 2022)
git_url: https://git.bioconductor.org/packages/CNEr
git_branch: master
git_last_commit: a9829eb
git_last_commit_date: 2022-04-26 11:17:50 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CNEr
Version: 1.33.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CNEr.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings CNEr_1.33.0.tar.gz
StartedAt: 2022-08-10 19:20:20 -0400 (Wed, 10 Aug 2022)
EndedAt: 2022-08-10 19:29:56 -0400 (Wed, 10 Aug 2022)
EllapsedTime: 576.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CNEr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CNEr.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings CNEr_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/CNEr.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNEr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNEr’ version ‘1.33.0’
* 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
* checking installed package size ... NOTE
  installed size is 18.6Mb
  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 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 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 ... 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 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.16-bioc/R/library/CNEr/libs/CNEr.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘rand’, possibly from ‘rand’ (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. 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     279.549  7.639 287.207
plotCNEWidth   5.502  0.068   5.569
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/CNEr.Rcheck/00check.log’
for details.



Installation output

CNEr.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL CNEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘CNEr’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/axt.c -o ucsc/axt.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/chain.c -o ucsc/chain.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/common.c -o ucsc/common.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/https.c -o ucsc/https.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/intExp.c -o ucsc/intExp.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I/usr/local/include  -g -fpic  -g -O2  -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(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 ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
 21.948   0.878  22.800 

Example timings

CNEr.Rcheck/CNEr-Ex.timings

nameusersystemelapsed
AssemblyStats0.0080.0040.011
Axt-class0.5720.0240.595
Axt-util0.0610.0120.073
CNE-class0.1880.0080.195
CNEDanRer10Hg380.0100.0000.009
CNEDensity0.6860.0120.699
GRangePairs-class0.6090.0040.613
addAncestorGO000
axisTrack0.0040.0000.004
axtChain000
axtInfo0.0010.0000.001
binner0.0010.0000.002
blatCNE000
ceScan-methods1.9130.0341.991
chainMergeSort0.0010.0000.000
chainNetSyntenic000
chainPreNet000
cneFinalListDanRer10Hg380.0230.0000.023
cneMerge1.3550.0041.358
fetchChromSizes000
fixCoordinates0.4510.0080.459
grangesPairsForDotplot0.0010.0000.002
last000
lastz000
lavToPsl0.0010.0000.000
makeAncoraFiles0.0330.0000.034
makeAxtTracks0.2690.0240.294
makeCNEDensity000
makeGRBs279.549 7.639287.207
matchDistribution0.2740.0000.274
netToAxt000
orgKEGGIds2EntrezIDs000
plotCNEDistribution0.4590.0040.463
plotCNEWidth5.5020.0685.569
psubAxt0.3740.0080.382
read.rmMask.GRanges0.0240.0000.024
read.rmskFasta0.0320.0000.032
readAncora0.0750.0000.076
readAncoraIntoSQLite0.9280.0000.929
readAxt0.0660.0040.070
readBed0.0740.0240.091
readCNERangesFromSQLite0.0890.0080.097
reverseCigar0.0010.0000.002
saveCNEToSQLite0.0970.0080.106
scoringMatrix0.0000.0000.001
subAxt-methods0.8870.0400.928
syntenicDotplot1.4910.2531.632
writeAxt0.0660.0120.077