Multiple platform build/check report for BioC 3.20 - BUILD BIN results for iCARE on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 iCARE on kjohnson3

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

Version: 1.34.0

Command: rm -rf iCARE.buildbin-libdir && mkdir iCARE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh iCARE_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R iCARE.buildbin-libdir

StartedAt: 2024-11-09 16:54:03 -0500 (Sat, 09 Nov 2024)

EndedAt: 2024-11-09 16:54:08 -0500 (Sat, 09 Nov 2024)

EllapsedTime: 4.1 seconds

RetCode: 0

Status: OK

PackageFile: iCARE_1.34.0.tgz

PackageFileSize: 1.504 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf iCARE.buildbin-libdir && mkdir iCARE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh iCARE_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R iCARE.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=iCARE.buildbin-libdir iCARE_1.34.0.tar.gz'
>>>>>>> 

* installing *source* package ‘iCARE’ ...
** using staged installation
** libs
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 source.c -o source.o
source.c:45:10: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
double * dVec_alloc(n, initFlag, initVal)
         ^
source.c:64:7: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int * iVec_alloc(n, initFlag, initVal)
      ^
source.c:81:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
double ** dMat_alloc(nrow, ncol, initFlag, initVal)
          ^
source.c:98:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void matrix_free(x, n)
     ^
source.c:114:12: 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_non_miss(vec, n, ovec)
           ^
source.c:135:13: 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 X_y(X, nr, nc, y, index, ni, ret)
            ^
source.c:155:13: 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 X_y2(X, nc, y, z, index, ni, ret)
            ^
source.c:185:15: 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 vec_mult(x, y, index, ni)
              ^
source.c:203:12: 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 vec_lteq_c(vec, n, c)
           ^
source.c:224:15: 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 mean_2val(vec, subvec, nsub, weights)
              ^
source.c:241:13: 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 mat_from_vec(vec, nr, nc, mat)
            ^
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 quant_vecs(probs, nprobs, n, ivec, lo, hi, h)
           ^
source.c:284:13: 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 quantile(x, n, probs, nprobs, lo, hi, h, ivec, ni, qs)
            ^
source.c:338:15: 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 var_dvec(vec, n)
              ^
source.c:358:12: 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_cutpoints(quantiles, nq, ref_LP, nref)
           ^
source.c:406:12: 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_miss_perc(cutpoints, ncuts, miss_LP)
           ^
source.c:427:12: 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 vec_ab(x, n, a, b)
           ^
source.c:444:13: 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_newEndpoints(cutpoints, ncuts, miss_LP, miss_perc, ref_LP, nref, rcut1, rcut2)
            ^
source.c:471:12: 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_subs_2cut(x, n, a, b, ret) 
           ^
source.c:493:13: 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_wgts(weights, subvec, nsub, retvec)
            ^
source.c:511:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ref_risk1(ref_risks, betavec, zmat, refmat, n_beta, nr_z, nc_z, nr_ref, nc_ref,
     ^
source.c:619:13: 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_int(nsub, age_new, t, aexp_rr, lambda, comp, zbeta, holder)
            ^
source.c:645:15: 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 finalVal(nsub, zbeta, expzbeta, age_new, age_int, lambda, loglambda, compRates, holder, tempv, weights)
              ^
source.c:684:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ref_risk2(betavec, zmat, refmat, n_beta, nr_z, nc_z, nr_ref, nc_ref,
     ^
24 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 iCARE.so source.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/iCARE.buildbin-libdir/00LOCK-iCARE/00new/iCARE/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (iCARE)


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

>>>>>>> Paths before fix:
iCARE.buildbin-libdir/iCARE/libs/iCARE.so:
	iCARE.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 4.4.1)
	/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" "iCARE.buildbin-libdir/iCARE/libs/iCARE.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "iCARE.buildbin-libdir/iCARE/libs/iCARE.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "iCARE.buildbin-libdir/iCARE/libs/iCARE.so"

>>>>>>> Paths after fix:
iCARE.buildbin-libdir/iCARE/libs/iCARE.so:
	iCARE.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 4.4.1)
	/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)