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Bioconductor / GenomicAlignments

Representation and manipulation of short genomic alignments
https://bioconductor.org/packages/GenomicAlignments
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install error #15

Closed shiyi-pan closed 2 years ago

shiyi-pan commented 4 years ago

Hi, I trid to install the package and met an error. My OS is Red Hat and GCC vresion is 8.3.0 and the package version is GenomicAlignments_1.10.1. I can't install the new version because of the limit of Rsamtools vresion could you help me fix this problem ? Thank you very much .

encodeOverlaps_methods.c: In function 'CharAE_append_int': encodeOverlaps_methods.c:49:2: warning: implicit declaration of function 'append_string_to_CharAE' [-Wimplicit-function-declaration] append_string_to_CharAE(char_ae, buf); ^~~~~~~ gcc -std=gnu99 -shared -fPIC -L/ds3512/home/panyp/ruanjian/packages/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o installing to /ds3512/home/panyp/ruanjian/R-4.0.3/lib64/R/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs R inst ** byte-compile and prepare package for lazy loading Warning: undefined slot classes in definition of "GAlignments": NAMES(class "characterORNULL") Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : methods can add arguments to the generic 'seqinfo<-' only if '...' is an argument to the generic Error: unable to load R code in package 'GenomicAlignments' Execution halted ERROR: lazy loading failed for package 'GenomicAlignments'

mtmorgan commented 4 years ago

Make sure that your installation is correct

BiocManager::valid()