Multiple platform build/check report for BioC 3.22 - BUILD results for CGEN on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4544
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4486
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4434
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*

BUILD results for CGEN on kjohnson3

To the developers/maintainers of the CGEN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGEN.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: CGEN

Version: 3.45.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CGEN

StartedAt: 2025-05-01 15:52:15 -0400 (Thu, 01 May 2025)

EndedAt: 2025-05-01 15:52:16 -0400 (Thu, 01 May 2025)

EllapsedTime: 1.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CGEN
###
##############################################################################
##############################################################################


* checking for file ‘CGEN/DESCRIPTION’ ... OK
* preparing ‘CGEN’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘CGEN’ ...
** this is package ‘CGEN’ version ‘3.45.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Additive.c -o Additive.o
Additive.c:103:21: error: unknown type name 'vec'
static void vecinit(vec, n, c)
                    ^
Additive.c:103:26: error: unknown type name 'n'
static void vecinit(vec, n, c)
                         ^
Additive.c:103:29: error: unknown type name 'c'
static void vecinit(vec, n, c)
                            ^
Additive.c:103:31: error: expected ';' after top level declarator
static void vecinit(vec, n, c)
                              ^
                              ;
Additive.c:107:1: error: expected identifier or '('
{
^
Additive.c:115:21: error: unknown type name 'invec'
static void vecmove(invec, n, outvec)
                    ^
Additive.c:115:28: error: unknown type name 'n'
static void vecmove(invec, n, outvec)
                           ^
Additive.c:115:31: error: unknown type name 'outvec'
static void vecmove(invec, n, outvec)
                              ^
Additive.c:115:38: error: expected ';' after top level declarator
static void vecmove(invec, n, outvec)
                                     ^
                                     ;
Additive.c:119:1: error: expected identifier or '('
{
^
Additive.c:130:24: error: unknown type name 'invec'
static void vecMultCon(invec, n, c, ret)
                       ^
Additive.c:130:31: error: unknown type name 'n'
static void vecMultCon(invec, n, c, ret)
                              ^
Additive.c:130:34: error: unknown type name 'c'
static void vecMultCon(invec, n, c, ret)
                                 ^
Additive.c:130:37: error: unknown type name 'ret'
static void vecMultCon(invec, n, c, ret)
                                    ^
Additive.c:130:41: error: expected ';' after top level declarator
static void vecMultCon(invec, n, c, ret)
                                        ^
                                        ;
Additive.c:135:1: error: expected identifier or '('
{  
^
Additive.c:144:26: error: unknown type name 'mat'
static void rMatMMultVec(mat, nrow, ncol, vec, ret)
                         ^
Additive.c:144:31: error: unknown type name 'nrow'
static void rMatMMultVec(mat, nrow, ncol, vec, ret)
                              ^
Additive.c:144:37: error: unknown type name 'ncol'
static void rMatMMultVec(mat, nrow, ncol, vec, ret)
                                    ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [Additive.o] Error 1
ERROR: compilation failed for package ‘CGEN’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmphfn8dJ/Rinst178221fe94d61/CGEN’
      -----------------------------------
ERROR: package installation failed