Multiple platform build/check report for BioC 3.20 - BUILD BIN results for SUITOR on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 BIN results for SUITOR on kjohnson1

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

Version: 1.8.0

Command: rm -rf SUITOR.buildbin-libdir && mkdir SUITOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SUITOR_1.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SUITOR.buildbin-libdir

StartedAt: 2024-12-21 16:53:37 -0500 (Sat, 21 Dec 2024)

EndedAt: 2024-12-21 16:53:46 -0500 (Sat, 21 Dec 2024)

EllapsedTime: 9.0 seconds

RetCode: 0

Status: OK

PackageFile: SUITOR_1.8.0.tgz

PackageFileSize: 306.9 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf SUITOR.buildbin-libdir && mkdir SUITOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SUITOR_1.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SUITOR.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SUITOR.buildbin-libdir SUITOR_1.8.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SUITOR’ ...
** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c SUITOR_init.c -o SUITOR_init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c source.c -o source.o
source.c:166:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double * dVec_alloc(n, initFlag, initVal)
                ^
source.c:185:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int * iVec_alloc(n, initFlag, initVal)
             ^
source.c:203:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static char * cVec_alloc(n, initFlag, initVal)
              ^
source.c:222:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void copy_dVec(v, n, ret)
            ^
source.c:233:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void matrixMult(m1, m1_nr, m1_nc, m2, m2_nc, ret)
            ^
source.c:256:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int which_max(v, n) 
           ^
source.c:280:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void which_max_cols(mat, nr, nc, ret) 
            ^
source.c:292:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int update_cons(cons, cons_len, index, nc)
           ^
source.c:323:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int myStopFun(cons, cons_len, inc, hMat, hnr, hnc, maxIndex) 
           ^
source.c:348:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void get_runif_vec(v, n, a, b)
            ^
source.c:359:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int get_idxMat0(idx, nr, nc, k, kfold) 
           ^
source.c:385:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double loglike(input, log_input, input_k_hat, idxMat, delta_denom, len, which_idx)
              ^
source.c:416:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void replaceZeroVal_dVec(v, n, minval)
            ^
source.c:428:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double get_delta_denom(v, n) 
              ^
source.c:444:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double get_max(v, n)
              ^
source.c:460:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void my_update_H(pV, w, h, wnr, wnc, hnc)
            ^
source.c:539:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void my_update_W(pV, w, h, wnr, wnc, hnc)
            ^
source.c:611:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void my_update_brunet(i, x, w, h, str)
            ^
source.c:636:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void get_init_WH(runifVec, w, h, wlen, hlen, maxval)
            ^
source.c:655:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void call_nmf(mat, str)
            ^
source.c:714:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void update_x_k(x_k, x_k_hat, idxMat, n)
            ^
source.c:838:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double get_median(v, n)
              ^
source.c:863:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void get_init_x_k(x, x_k, idxMat, nr, nc, tmpvec, minvalue)
            ^
source.c:916:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void get_colsums(x, nr, nc, ret)
            ^
source.c:934:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void transpose(v, nr, nc, ret)
            ^
source.c:949:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void ECM_update_h(h1, h0, w0, x_k, hnr, hnc, wnr, wnc, xnr, xnc, vM, vN, vN2)
            ^
source.c:983:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void ECM_update_w(w1, h1, w0, x_k, hnr, hnc, wnr, wnc, xnr, xnc, vM, vN, vN2)
            ^
source.c:1017:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int ECM_alg(str)
           ^
source.c:1093:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void init_wh_rank(str, rank)
            ^
source.c:1119:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void suitor_main(str)
            ^
source.c:1203:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void init_logx(x, logx, n)
            ^
source.c:1221:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void NMFSTR_init(str, iargs, dargs, xmat) 
            ^
source.c:1311:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void NMFSTR_free(str, EMflag)
            ^
source.c:1339:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void C_call_nmf(mat, iargs, dargs, retW, retH)
     ^
source.c:1361:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void C_call_suitor(mat, iargs, dargs, rankVec, kVec, ret_train, ret_test, ret_convVec, ret_EM_niterVec)
     ^
35 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SUITOR.so SUITOR_init.o source.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/SUITOR.buildbin-libdir/00LOCK-SUITOR/00new/SUITOR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SUITOR)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so
>>>>>>> 

>>>>>>> Paths before fix:
SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so:
	SUITOR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so"

>>>>>>> Paths after fix:
SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so:
	SUITOR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)