* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘WebGestaltR’ ...
** this is package ‘WebGestaltR’ version ‘1.0.1’
** package ‘WebGestaltR’ successfully unpacked and MD5 sums checked
** using staged installation
*** Checking if cargo is installed
*** Checking if cargo is newer than the required version
*** cargo is ok
*** linker supports --wrap; excluding libc exit/abort from the symbol table
** libs
using C compiler: ‘gcc-15 (Debian 15.3.0-2) 15.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpaYDKrE/R.INSTALL1319b1208a1d6f/WebGestaltR/src'
rm -Rf WebGestaltR.so ./rust/target/release/libWebGestaltR.a entrypoint.o wrapstubs.o
gcc-15 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c entrypoint.c -o entrypoint.o
gcc-15 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wrapstubs.c -o wrapstubs.o
rustc 1.95.0 (59807616e 2026-04-14) (built from a source tarball)
if [ "yes" = "yes" ]; then \
/usr/bin/tar --extract --xz -f ./rust/vendor.tar.xz -C ./rust && \
mkdir -p ./.cargo && \
cp ./config.toml ./.cargo/config.toml; \
fi
# In some environments, ~/.cargo/bin might not be included in PATH, so we need
# to set it here to ensure cargo can be invoked. It is appended to PATH and
# therefore is only used if cargo is absent from the user's PATH.
if [ "" != "true" ]; then \
export CARGO_HOME=/home/hornik/tmp/scratch/RtmpaYDKrE/R.INSTALL1319b1208a1d6f/WebGestaltR/src/.cargo; \
fi && \
export CARGO_HOME="/home/hornik/tmp/scratch/RtmpaYDKrE/R.INSTALL1319b1208a1d6f/WebGestaltR/src/.cargo" && export PATH="/home/hornik/bin:/usr/local/bin:/usr/bin:/bin:/home/hornik/.cargo/bin" &&\
cargo build --lib --jobs 2 --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target --offline
Compiling autocfg v1.5.0
Compiling proc-macro2 v1.0.103
Compiling unicode-ident v1.0.22
Compiling quote v1.0.42
Compiling libm v0.2.15
Compiling num-traits v0.2.19
Compiling libc v0.2.178
Compiling cfg-if v1.0.4
Compiling zerocopy v0.8.31
Compiling getrandom v0.2.16
Compiling crossbeam-utils v0.8.21
Compiling paste v1.0.15
Compiling rand_core v0.6.4
Compiling syn v2.0.111
Compiling ppv-lite86 v0.2.21
Compiling matrixmultiply v0.3.10
Compiling serde_core v1.0.228
Compiling syn v1.0.109
Compiling bytemuck v1.24.0
Compiling safe_arch v0.7.4
Compiling rand_chacha v0.3.1
Compiling crossbeam-epoch v0.9.18
Compiling num-complex v0.4.6
Compiling num-integer v0.1.46
Compiling rawpointer v0.2.1
Compiling rayon-core v1.13.0
Compiling typenum v1.19.0
Compiling crossbeam-deque v0.8.6
Compiling rand v0.8.5
Compiling wide v0.7.33
Compiling approx v0.5.1
Compiling extendr-ffi v0.9.0
Compiling memchr v2.7.6
Compiling version_check v0.9.5
Compiling ahash v0.8.11
Compiling nalgebra-macros v0.1.0
Compiling simba v0.6.0
Compiling rand_distr v0.4.3
Compiling num-rational v0.4.2
Compiling serde v1.0.228
Compiling ryu v1.0.20
Compiling either v1.15.0
Compiling itoa v1.0.15
Compiling once_cell v1.21.3
Compiling serde_json v1.0.145
Compiling rayon v1.11.0
Compiling nalgebra v0.29.0
Compiling csv-core v0.1.13
Compiling serde_derive v1.0.228
Compiling zerocopy v0.7.35
Compiling lazy_static v1.5.0
Compiling extendr-api v0.9.0
Compiling extendr-macros v0.9.0
Compiling statrs v0.16.1
Compiling csv v1.4.0
Compiling ndarray v0.15.6
Compiling readonly v0.2.13
Compiling webgestalt_lib v0.3.2 (https://github.com/bzhanglab/webgestalt_rust.git?branch=master#6f5f8fac)
Compiling WebGestaltR v0.1.0 (/home/hornik/tmp/scratch/RtmpaYDKrE/R.INSTALL1319b1208a1d6f/WebGestaltR/src/rust)
Finished `release` profile [optimized] target(s) in 1m 37s
if [ "" != "true" ]; then \
rm -Rf /home/hornik/tmp/scratch/RtmpaYDKrE/R.INSTALL1319b1208a1d6f/WebGestaltR/src/.cargo && \
rm -Rf ./rust/target/release/build; \
fi
gcc-15 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o WebGestaltR.so entrypoint.o wrapstubs.o -L./rust/target/release -lWebGestaltR -Wl,--wrap=exit -Wl,--wrap=_exit -Wl,--wrap=abort -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpaYDKrE/R.INSTALL1319b1208a1d6f/WebGestaltR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpaYDKrE/R.INSTALL1319b1208a1d6f/WebGestaltR/src'
/usr/bin/nm: apple_versioning.c.o: no symbols
/usr/bin/nm: os_version_check.c.o: no symbols
/usr/bin/nm: trampoline_setup.c.o: no symbols
/usr/bin/nm: truncxfbf2.c.o: no symbols
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpaYDKrE/R.INSTALL1319b1208a1d6f/WebGestaltR/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-WebGestaltR/00new/WebGestaltR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘WebGestaltR’
finding HTML links ... done
WebGestaltR html
WebGestaltRMultiOmics html
WebGestaltRMultiOmicsGSEA html
WebGestaltRMultiOmicsOra html
affinityPropagation html
cacheUrl html
createMetaReport html
createMetaSummaryReport html
createNtaReport html
createReport html
enrichResultSection html
expandDag html
fill_input_data_frame html
formatCheck html
goSlimSummary html
gsea_rust html
idMapping html
jaccardSim html
kMedoid html
keepRep html
linkModification html
listArchiveUrl html
listGeneSet html
listIdType html
listOrganism html
listReferenceSet html
loadGeneSet html
metaEnrichResultSection html
metaLinkModification html
metaSummaryDescription html
multiswGsea html
nta_rust html
ora_rust html
prepareGseaInput html
prepareInputMatrixGsea html
readGmt html
rust_multiomics_ora html
specificParameterSummaryGsea html
specificParameterSummaryOra html
summaryDescription html
swGsea html
weightedSetCover html
** 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 (WebGestaltR)