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This page was generated on 2025-03-19 11:43 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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Package 387/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.farms 1.55.0  (landing page)
Andreas Mitterecker
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/cn.farms
git_branch: devel
git_last_commit: 8600141
git_last_commit_date: 2024-10-29 09:36:23 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped

INSTALL results for cn.farms on lconway

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.

raw results


Summary

Package: cn.farms
Version: 1.55.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cn.farms
StartedAt: 2025-03-18 15:31:57 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 15:32:01 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 3.8 seconds
RetCode: 1
Status:   ERROR  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cn.farms
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘cn.farms’ ...
** this is package ‘cn.farms’ version ‘1.55.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_cnfarms.c -o R_init_cnfarms.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sparse_farms.c -o sparse_farms.o
sparse_farms.c:185:13: error: implicit declaration of function 'Calloc' is invalid in C99 [-Werror,-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: implicit declaration of function 'Calloc' is invalid in C99 [-Werror,-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: implicit declaration of function 'Free' is invalid in C99 [-Werror,-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: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
                Free(E_SX_n[l]);
                ^
sparse_farms.c:654:2: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        Free(ret[3]);
        ^
sparse_farms.c:683:3: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
                Free(E_SX_n[l]);
                ^
sparse_farms.c:687:2: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        Free(ret[1]);
        ^
19 errors generated.
make: *** [sparse_farms.o] Error 1
ERROR: compilation failed for package ‘cn.farms’
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cn.farms’