x86_64-conda-linux-gnu-cc -I"/opt/conda/envs/env_tih_hrd_running_env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/envs/env_tih_hrd_running_env/include -I/opt/conda/envs/env_tih_hrd_running_env/include -Wl,-rpath-link,/opt/conda/envs/env_tih_hrd_running_env/lib    -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/env_tih_hrd_running_env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1763744062972/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=/opt/conda/envs/env_tih_hrd_running_env=/usr/local/src/conda-prefix  -c 000.init.c -o 000.init.o
x86_64-conda-linux-gnu-cc -shared -L/opt/conda/envs/env_tih_hrd_running_env/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/envs/env_tih_hrd_running_env/lib -Wl,-rpath-link,/opt/conda/envs/env_tih_hrd_running_env/lib -L/opt/conda/envs/env_tih_hrd_running_env/lib -o HRDscoreAlteraBam.so 000.init.o cbs2rank.o rshared.o scansnp-random.o -lgfortran -lm -lquadmath -L/opt/conda/envs/env_tih_hrd_running_env/lib/R/lib -lR
No man pages found in package  'HRDscoreAlteraBam' 
 Tumor bam =  
 Normal bam =  
 FACETS pileup = HCC1395_tumor_vs_HCC1395_BL.pileup.csv.gz 
 Bypass segments =  
 Bypass ploidy =  
 Somatic vcf = HCC1395_tumor_vs_HCC1395_BL.vcf.gz 
 Starting from:  pileup 
Skipping CNV signatures ploidy adjustment (adjust_ploidy = FALSE or not set)
QC status: review (score=70, issues: Extreme |dipLogR| (>0.35): possible baseline mis-centering)