Multiple platform build/check report for BioC 3.20 - INSTALL results for iCARE 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*

INSTALL results for iCARE on kjohnson1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iCARE

StartedAt: 2024-12-30 16:57:13 -0500 (Mon, 30 Dec 2024)

EndedAt: 2024-12-30 16:57:23 -0500 (Mon, 30 Dec 2024)

EllapsedTime: 9.8 seconds

RetCode: 0

Status: OK

Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘iCARE’ ...
** 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 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 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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)