| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 392/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cn.farms 1.56.0 (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. |
| Package: cn.farms |
| Version: 1.56.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cn.farms |
| StartedAt: 2025-04-21 15:56:30 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 15:56:31 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 1.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/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 ‘1.56.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_cnfarms.c -o R_init_cnfarms.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c laplace.cpp -o laplace.o
laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(argLeft >= 0.0 && argRight >= 0.0) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
laplace.cpp:364:36: note: uninitialized use occurs here
double I2left=(-leftMy/leftSigma)*I1left+I0left;
^~~~~~
laplace.cpp:275:7: note: remove the 'if' if its condition is always true
else if(argLeft >= 0.0 && argRight >= 0.0) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
else if(argLeft >= 0.0 && argRight >= 0.0) {
^~~~~~~~~~~~~~
laplace.cpp:364:36: note: uninitialized use occurs here
double I2left=(-leftMy/leftSigma)*I1left+I0left;
^~~~~~
laplace.cpp:275:10: note: remove the '&&' if its condition is always true
else if(argLeft >= 0.0 && argRight >= 0.0) {
^~~~~~~~~~~~~~~~~
laplace.cpp:198:15: note: initialize the variable 'I1left' to silence this warning
double I1left;
^
= 0.0
laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(argLeft >= 0.0 && argRight >= 0.0) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
laplace.cpp:365:39: note: uninitialized use occurs here
double I2right=(-rightMy/rightSigma)*I1right+I0right;
^~~~~~~
laplace.cpp:275:7: note: remove the 'if' if its condition is always true
else if(argLeft >= 0.0 && argRight >= 0.0) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
else if(argLeft >= 0.0 && argRight >= 0.0) {
^~~~~~~~~~~~~~
laplace.cpp:365:39: note: uninitialized use occurs here
double I2right=(-rightMy/rightSigma)*I1right+I0right;
^~~~~~~
laplace.cpp:275:10: note: remove the '&&' if its condition is always true
else if(argLeft >= 0.0 && argRight >= 0.0) {
^~~~~~~~~~~~~~~~~
laplace.cpp:199:16: note: initialize the variable 'I1right' to silence this warning
double I1right;
^
= 0.0
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
int method=0;
^
laplace.cpp:23:11: warning: unused variable 'steps' [-Wunused-const-variable]
const int steps=30;
^
laplace.cpp:26:14: warning: unused variable 'integrationFailureFactor' [-Wunused-const-variable]
const double integrationFailureFactor=5.0;
^
laplace.cpp:27:14: warning: unused variable 'sigmaFactor' [-Wunused-const-variable]
const double sigmaFactor=0.1;
^
laplace.cpp:30:14: warning: unused variable 'Pi' [-Wunused-const-variable]
const double Pi=M_PI;
^
laplace.cpp:31:14: warning: unused variable 'E' [-Wunused-const-variable]
const double E=M_E;
^
laplace.cpp:34:14: warning: unused variable 'sqrt3' [-Wunused-const-variable]
const double sqrt3=1.7320508075688772935274463415058723669428052538104;
^
laplace.cpp:35:14: warning: unused variable 'sqrt2Pi' [-Wunused-const-variable]
const double sqrt2Pi=2.5066282746310005024157652848110452530069867406099;
^
12 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sparse_farms.c -o sparse_farms.o
sparse_farms.c:185:13: error: call to undeclared function 'Calloc'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
void** ret=Calloc(1, void*);
^
sparse_farms.c:185:23: error: expected expression
void** ret=Calloc(1, void*);
^
sparse_farms.c:189:31: error: expected expression
E_SX_n =(double**)Calloc(nn, double*);
^
sparse_farms.c:198:22: error: expected expression
nna=(int*)Calloc(1, int);
^
sparse_farms.c:204:32: error: expected expression
E_SX_n[l]=(double*)Calloc(3, double);
^
sparse_farms.c:264:13: error: call to undeclared function 'Calloc'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
void** ret=Calloc(4, void*);
^
sparse_farms.c:264:23: error: expected expression
void** ret=Calloc(4, void*);
^
sparse_farms.c:272:22: error: expected expression
nna=(int*)Calloc(1, int);
^
sparse_farms.c:277:24: error: expected expression
L=(double**)Calloc(2, double*);
^
sparse_farms.c:279:29: error: expected expression
lapla=(double**)Calloc(nn, double*);
^
sparse_farms.c:281:31: error: expected expression
E_SX_n =(double**)Calloc(nn, double*);
^
sparse_farms.c:287:27: error: expected expression
L[l]=(double*)Calloc(3, double);
^
sparse_farms.c:295:31: error: expected expression
lapla[l]=(double*)Calloc(3, double);
^
sparse_farms.c:297:32: error: expected expression
E_SX_n[l]=(double*)Calloc(3, double);
^
sparse_farms.c:642:3: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
Free(L[l]);
^
sparse_farms.c:642:3: note: did you mean 'free'?
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/malloc/_malloc.h:42:7: note: 'free' declared here
void free(void *);
^
sparse_farms.c:648:3: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
Free(E_SX_n[l]);
^
sparse_farms.c:654:2: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
Free(ret[3]);
^
sparse_farms.c:683:3: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
Free(E_SX_n[l]);
^
sparse_farms.c:687:2: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
Free(ret[1]);
^
19 errors generated.
make: *** [sparse_farms.o] Error 1
ERROR: compilation failed for package ‘cn.farms’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpINSA8u/Rinst15e5c41e4ddf4/cn.farms’
-----------------------------------
ERROR: package installation failed