Ge Tan
| Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025) |
| git_url: https://git.bioconductor.org/packages/CNEr |
| git_branch: RELEASE_3_21 |
| git_last_commit: 7ed6d82 |
| git_last_commit_date: 2025-04-15 10:28:43 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 395/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNEr 1.44.0 (landing page) Ge Tan
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
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: 1.44.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CNEr |
| StartedAt: 2025-07-31 21:20:46 -0400 (Thu, 31 Jul 2025) |
| EndedAt: 2025-07-31 21:20:52 -0400 (Thu, 31 Jul 2025) |
| EllapsedTime: 5.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CNEr
###
##############################################################################
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* checking for file ‘CNEr/DESCRIPTION’ ... OK
* preparing ‘CNEr’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘CNEr’ ...
** this is package ‘CNEr’ version ‘1.44.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_CNEr.c -o R_init_CNEr.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
int _binFirstShift = binFirstShift();
^
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
int _binNextShift = binNextShift();
^
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/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:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
struct slThreshold *thresholds, *nextThreshold, *el_threshold;
^
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE, *nextCNE, *el_CNE;
^
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE;
^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
int nrThresholds = GET_LENGTH(winSize);
^
8 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/axt.c -o ucsc/axt.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/base64.c -o ucsc/base64.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/binRange.c -o ucsc/binRange.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bits.c -o ucsc/bits.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/chain.c -o ucsc/chain.o
ucsc/chain.c:399:5: warning: variable 'usedCount' set but not used [-Wunused-but-set-variable]
int usedCount = 0, count = 0;
^
ucsc/chain.c:399:20: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int usedCount = 0, count = 0;
^
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:360:14: error: too many arguments to function call, expected 0, have 1
free(el);
~~~~ ^~
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 and 1 error generated.
make: *** [ucsc/common.o] Error 1
ERROR: compilation failed for package ‘CNEr’
* removing ‘/private/tmp/RtmpFPZ92H/Rinst13d445e639790/CNEr’
-----------------------------------
ERROR: package installation failed