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rnabioco / raer

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments
https://rnabioco.github.io/raer/
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devtools build utilities issue load_all and check error #12

Closed kriemo closed 2 years ago

kriemo commented 2 years ago

The typical devtools utilities in Rstudio throw a strange error. All the following commands (or macOS shortcuts) recompile the package even with no changes to any code, then throw a normalizePath error. I don't see this in github actions or when using install + restart or clean and rebuild. 

library(devtools)
#> Loading required package: usethis
load_all("~/rbi/src/raer")
#> ℹ Loading raer
#> Exports from /Users/kriemo/rbi/src/raer/src/bam_reader.cpp:
#>    DataFrame read_bam_tags(std::string bampath, std::vector<std::string> tag_ids, std::vector<std::string> tag_types, std::string region = ".")
#>    DataFrame read_bam(std::string bampath, std::vector<std::string> tag_ids, std::vector<std::string> tag_types, std::string region = ".")
#> 
#> Exports from /Users/kriemo/rbi/src/raer/src/plp.cpp:
#>    int run_pileup(std::string bampath, std::string fapath, std::string region, std::string outfn, std::string bedfn, int min_reads = 20, int max_depth = 10000, int min_baseQ = 20, std::string libtype = "fr-first-strand")
#>    List get_region(std::string region)
#> 
#> Exports from /Users/kriemo/rbi/src/raer/src/scidx.cpp:
#>    int build_index(std::string bampath, std::string idxpath)
#>    int fetch_cb_reads(std::string bampath, std::string outpath, std::vector<std::string> vals)
#> 
#> /Users/kriemo/rbi/src/raer/src/RcppExports.cpp updated.
#> /Users/kriemo/rbi/src/raer/R/RcppExports.R updated.
#> Re-compiling raer
#> * installing *source* package ‘raer’ ...
#> ** using staged installation
#> ** libs
#> /opt/homebrew/bin/ccache g++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
#> /opt/homebrew/bin/ccache g++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_reader.cpp -o bam_reader.o
#> /opt/homebrew/bin/ccache gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bedidx.c -o bedidx.o
#> bedidx.c:40:1: warning: unused function 'ks_getc' [-Wunused-function]
#> KSTREAM_INIT(gzFile, gzread, 8192)
#> ^
#> /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:154:49: note: expanded from macro 'KSTREAM_INIT'
#> #define KSTREAM_INIT(type_t, __read, __bufsize) KSTREAM_INIT2(static, type_t, __read, __bufsize)
#>                                                 ^
#> /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:152:2: note: expanded from macro 'KSTREAM_INIT2'
#>         __KS_INLINED(__read)
#>         ^
#> /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:68:20: note: expanded from macro '__KS_INLINED'
#>         static inline int ks_getc(kstream_t *ks) \
#>                           ^
#> 1 warning generated.
#> /opt/homebrew/bin/ccache gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bri_get.c -o bri_get.o
#> /opt/homebrew/bin/ccache gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bri_index.c -o bri_index.o
#> /opt/homebrew/bin/ccache gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bri_main.c -o bri_main.o
#> /opt/homebrew/bin/ccache gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bri_show.c -o bri_show.o
#> /opt/homebrew/bin/ccache gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bri_test.c -o bri_test.o
#> /opt/homebrew/bin/ccache gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cplp.c -o cplp.o
#> /opt/homebrew/bin/ccache g++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c plp.cpp -o plp.o
#> /opt/homebrew/bin/ccache g++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64  -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c scidx.cpp -o scidx.o
#> /opt/homebrew/bin/ccache g++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o raer.so RcppExports.o bam_reader.o bedidx.o bri_get.o bri_index.o bri_main.o bri_show.o bri_test.o cplp.o plp.o scidx.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
#> installing to /private/var/folders/r9/g3c47jrj40gc14d8qsqx7src0000gn/T/RtmpkoN1UP/devtools_install_904b3d24ad87/00LOCK-raer/00new/raer/libs
#> ** checking absolute paths in shared objects and dynamic libraries
#> * DONE (raer)
#> Error in normalizePath(path, winslash = "/", mustWork = TRUE): path[1]="/var/folders/r9/g3c47jrj40gc14d8qsqx7src0000gn/T//RtmpkoN1UP/devtools_install_904b3d24ad87/raer ": No such file or directory

Created on 2022-02-14 by the reprex package (v2.0.1)

kwells4 commented 2 years ago

The error also happened outside of Rstudio for me, so not necessarily associated with Rstudio. I also tried in just in the terminal and in the terminal in an anaconda envrionment and got the same errors.