| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-22 11:46 -0400 (Sat, 22 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4547 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| 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 387/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cn.farms 1.55.0 (landing page) Andreas Mitterecker
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the cn.farms package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cn.farms.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. |
| Package: cn.farms |
| Version: 1.55.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data cn.farms |
| StartedAt: 2025-03-21 21:49:50 -0000 (Fri, 21 Mar 2025) |
| EndedAt: 2025-03-21 21:49:53 -0000 (Fri, 21 Mar 2025) |
| EllapsedTime: 3.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data cn.farms
###
##############################################################################
##############################################################################
* checking for file ‘cn.farms/DESCRIPTION’ ... OK
* preparing ‘cn.farms’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘cn.farms’ ...
** this is package ‘cn.farms’ version ‘1.55.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c R_init_cnfarms.c -o R_init_cnfarms.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
laplace.cpp:442:13: warning: unused variable ‘method’ [-Wunused-variable]
442 | int method=0;
| ^~~~~~
laplace.cpp: In function ‘void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)’:
laplace.cpp:367:16: warning: ‘I1left’ may be used uninitialized [-Wmaybe-uninitialized]
367 | double leftMoment1=1.0*leftMy*I0left+1.0*leftSigma*I1left;
| ^~~~~~~~~~~
laplace.cpp:198:16: note: ‘I1left’ was declared here
198 | double I1left;
| ^~~~~~
laplace.cpp:387:35: warning: ‘I1right’ may be used uninitialized [-Wmaybe-uninitialized]
387 | absMoment1=(I1right*leftMy+I1left*rightMy+2.0*I1left*I1right*leftSigma)/(I1left-I1right);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
laplace.cpp:199:16: note: ‘I1right’ was declared here
199 | double I1right;
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c sparse_farms.c -o sparse_farms.o
sparse_farms.c: In function ‘normData’:
sparse_farms.c:185:20: error: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration]
185 | void** ret=Calloc(1, void*);
| ^~~~~~
| calloc
sparse_farms.c:185:30: error: expected expression before ‘void’
185 | void** ret=Calloc(1, void*);
| ^~~~
sparse_farms.c:189:39: error: expected expression before ‘double’
189 | E_SX_n =(double**)Calloc(nn, double*);
| ^~~~~~
sparse_farms.c:198:29: error: expected expression before ‘int’
198 | nna=(int*)Calloc(1, int);
| ^~~
sparse_farms.c:204:46: error: expected expression before ‘double’
204 | E_SX_n[l]=(double*)Calloc(3, double);
| ^~~~~~
sparse_farms.c: In function ‘sparseFarmsC’:
sparse_farms.c:264:30: error: expected expression before ‘void’
264 | void** ret=Calloc(4, void*);
| ^~~~
sparse_farms.c:272:29: error: expected expression before ‘int’
272 | nna=(int*)Calloc(1, int);
| ^~~
sparse_farms.c:277:31: error: expected expression before ‘double’
277 | L=(double**)Calloc(2, double*);
| ^~~~~~
sparse_farms.c:279:36: error: expected expression before ‘double’
279 | lapla=(double**)Calloc(nn, double*);
| ^~~~~~
sparse_farms.c:281:39: error: expected expression before ‘double’
281 | E_SX_n =(double**)Calloc(nn, double*);
| ^~~~~~
sparse_farms.c:287:41: error: expected expression before ‘double’
287 | L[l]=(double*)Calloc(3, double);
| ^~~~~~
sparse_farms.c:295:45: error: expected expression before ‘double’
295 | lapla[l]=(double*)Calloc(3, double);
| ^~~~~~
sparse_farms.c:297:46: error: expected expression before ‘double’
297 | E_SX_n[l]=(double*)Calloc(3, double);
| ^~~~~~
sparse_farms.c: In function ‘deinit’:
sparse_farms.c:642:17: error: implicit declaration of function ‘Free’; did you mean ‘free’? [-Wimplicit-function-declaration]
642 | Free(L[l]);
| ^~~~
| free
make: *** [/home/biocbuild/R/R/etc/Makeconf:201: sparse_farms.o] Error 1
ERROR: compilation failed for package ‘cn.farms’
* removing ‘/home/biocbuild/tmp/RtmpyAYwLB/Rinst292b849d682f6/cn.farms’
-----------------------------------
ERROR: package installation failed