Ge Tan
| Snapshot Date: 2025-02-14 13:40 -0500 (Fri, 14 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/CNEr |
| git_branch: devel |
| git_last_commit: 7b0cff1 |
| git_last_commit_date: 2024-10-29 09:50:06 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-15 11:42 -0500 (Sat, 15 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| 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 387/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNEr 1.43.0 (landing page) Ge Tan
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
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. |
| Package: CNEr |
| Version: 1.43.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNEr_1.43.0.tar.gz |
| StartedAt: 2025-02-14 19:31:18 -0500 (Fri, 14 Feb 2025) |
| EndedAt: 2025-02-14 19:41:24 -0500 (Fri, 14 Feb 2025) |
| EllapsedTime: 606.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CNEr.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNEr_1.43.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNEr.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNEr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNEr’ version ‘1.43.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
installed size is 17.7Mb
sub-directories of 1Mb or more:
extdata 15.9Mb
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
GRangePairs-class.Rd: GRanges, GRangesList
readBed.Rd: import.bed
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/CNEr/libs/CNEr.so’:
Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
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)
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 252.966 4.415 258.596
plotCNEWidth 6.530 0.318 6.915
* 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
‘/Users/biocbuild/bbs-3.21-bioc/meat/CNEr.Rcheck/00check.log’
for details.
CNEr.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNEr
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘CNEr’ ...
** this is package ‘CNEr’ version ‘1.43.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_CNEr.c -o R_init_CNEr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
int _binNextShift = binNextShift();
^
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
int _binFirstShift = binFirstShift();
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c io.c -o io.o
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
struct axt *axt=NULL, *curAxt;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ceScan.c -o ceScan.o
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
int i, n;
^
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
char rest, path[PATH_LEN];
^
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE, *nextCNE, *el_CNE;
^
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
struct slThreshold *thresholds, *nextThreshold, *el_threshold;
^
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE;
^
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
int nrThresholds = GET_LENGTH(winSize);
^
8 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/axt.c -o ucsc/axt.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/base64.c -o ucsc/base64.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/binRange.c -o ucsc/binRange.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bits.c -o ucsc/bits.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/chain.c -o ucsc/chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c:475:16: warning: unused function 'cirTreeOverlaps' [-Wunused-function]
INLINE boolean cirTreeOverlaps(int qChrom, int qStart, int qEnd,
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:1982:18: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*in == '"'))
~~~~^~~~~~
ucsc/common.c:1982:18: note: remove extraneous parentheses around the comparison to silence this warning
if ((*in == '"'))
~ ^ ~
ucsc/common.c:1982:18: note: use '=' to turn this equality comparison into an assignment
if ((*in == '"'))
^~
=
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
int pastPoly = 0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/hash.c -o ucsc/hash.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/https.c -o ucsc/https.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/intExp.c -o ucsc/intExp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/kxTok.c -o ucsc/kxTok.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/options.c -o ucsc/options.o
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
long long discardMe = 0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/sqlList.c -o ucsc/sqlList.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/os.c -o ucsc/os.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)
CNEr.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
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Platform: x86_64-apple-darwin20
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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> 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
23.819 1.099 25.033
CNEr.Rcheck/CNEr-Ex.timings
| name | user | system | elapsed | |
| AssemblyStats | 0.016 | 0.033 | 0.085 | |
| Axt-class | 0.822 | 0.031 | 0.856 | |
| Axt-util | 0.086 | 0.002 | 0.089 | |
| CNE-class | 0.239 | 0.014 | 0.256 | |
| CNEDanRer10Hg38 | 0.010 | 0.001 | 0.012 | |
| CNEDensity | 0.702 | 0.041 | 0.749 | |
| GRangePairs-class | 0.721 | 0.022 | 0.747 | |
| addAncestorGO | 0 | 0 | 0 | |
| axisTrack | 0.005 | 0.004 | 0.008 | |
| axtChain | 0.001 | 0.000 | 0.000 | |
| axtInfo | 0.001 | 0.000 | 0.002 | |
| binner | 0.002 | 0.000 | 0.002 | |
| blatCNE | 0.000 | 0.001 | 0.000 | |
| ceScan-methods | 2.698 | 0.173 | 2.879 | |
| chainMergeSort | 0 | 0 | 0 | |
| chainNetSyntenic | 0.000 | 0.001 | 0.000 | |
| chainPreNet | 0 | 0 | 0 | |
| cneFinalListDanRer10Hg38 | 0.023 | 0.002 | 0.025 | |
| cneMerge | 0.543 | 0.059 | 0.605 | |
| fetchChromSizes | 0 | 0 | 0 | |
| fixCoordinates | 0.588 | 0.045 | 0.637 | |
| grangesPairsForDotplot | 0.001 | 0.001 | 0.003 | |
| last | 0.000 | 0.001 | 0.000 | |
| lastz | 0.000 | 0.001 | 0.000 | |
| lavToPsl | 0 | 0 | 0 | |
| makeAncoraFiles | 0.035 | 0.002 | 0.037 | |
| makeAxtTracks | 0.266 | 0.009 | 0.277 | |
| makeCNEDensity | 0.000 | 0.001 | 0.001 | |
| makeGRBs | 252.966 | 4.415 | 258.596 | |
| matchDistribution | 0.355 | 0.025 | 0.382 | |
| netToAxt | 0 | 0 | 0 | |
| orgKEGGIds2EntrezIDs | 0.000 | 0.001 | 0.001 | |
| plotCNEDistribution | 0.499 | 0.011 | 0.512 | |
| plotCNEWidth | 6.530 | 0.318 | 6.915 | |
| psubAxt | 0.447 | 0.020 | 0.468 | |
| read.rmMask.GRanges | 0.026 | 0.003 | 0.030 | |
| read.rmskFasta | 0.031 | 0.002 | 0.033 | |
| readAncora | 0.082 | 0.002 | 0.085 | |
| readAncoraIntoSQLite | 0.940 | 0.027 | 0.980 | |
| readAxt | 0.083 | 0.015 | 0.100 | |
| readBed | 0.069 | 0.011 | 0.074 | |
| readCNERangesFromSQLite | 0.092 | 0.009 | 0.101 | |
| reverseCigar | 0.002 | 0.000 | 0.002 | |
| saveCNEToSQLite | 0.117 | 0.009 | 0.128 | |
| scoringMatrix | 0.001 | 0.000 | 0.001 | |
| subAxt-methods | 1.029 | 0.044 | 1.080 | |
| syntenicDotplot | 1.746 | 0.423 | 2.104 | |
| writeAxt | 0.075 | 0.008 | 0.084 | |