ERROR: lazy loading failed for package 'QuasR'
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@hackerzone85-10021
Last seen 3.6 years ago
I have faced problem when trying to installing QuasR from github using install_github()
Installing package into ‘C:/Users/BLAB-2/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
* installing *source* package 'QuasR' ...
** libs
g++ -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c R_init_QuasR.cpp -o R_init_QuasR.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c cat_bam.c -o cat_bam.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c count_alignments.c -o count_alignments.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c count_junctions.cpp -o count_junctions.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c export_wig.c -o export_wig.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c idxstats_bam.c -o idxstats_bam.o
g++ -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c profile_alignments.c -o profile_alignments.o
g++ -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c quantify_methylation.cpp -o quantify_methylation.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c split_sam_chr.c -o split_sam_chr.o
gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include"   -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
g++ -m32 -shared -s -static-libgcc -o QuasR.dll tmp.def R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/usrlib/i386/libbam.a C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/usrlib/i386/libbam.a C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/usrlib/i386/libbcf.a C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LC:/PROGRA~1/R/R-32~1.4/bin/i386 -lR
installing to C:/Users/BLAB-2/Documents/R/win-library/3.2/QuasR/libs/i386
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace 'S4Vectors' 0.8.11 is already loaded, but >= 0.9.25 is required
ERROR: lazy loading failed for package 'QuasR'
* removing 'C:/Users/BLAB-2/Documents/R/win-library/3.2/QuasR'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-32~1.4/bin/i386/R" CMD INSTALL -l "C:\Users\BLAB-2\Documents\R\win-library\3.2" "C:/Users/BLAB-2/Downloads/Compressed/QuasR_1.11.2.tar.gz"' had status 1
Warning in install.packages :
  installation of package ‘C:/Users/BLAB-2/Downloads/Compressed/QuasR_1.11.2.tar.gz’ had non-zero exit status

sessioninfo:

R version 3.2.4 Revised (2016-03-16 r70336)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] DESeq2_1.10.1              RcppArmadillo_0.6.600.4.0 
 [3] Rcpp_0.12.4                SummarizedExperiment_1.0.2
 [5] Biobase_2.30.0             GenomicRanges_1.22.4      
 [7] GenomeInfoDb_1.6.3         IRanges_2.4.8             
 [9] S4Vectors_0.8.11           BiocGenerics_0.16.1       
[11] BiocInstaller_1.20.1      

loaded via a namespace (and not attached):
 [1] Formula_1.2-1        DBI_0.3.1            ggplot2_2.1.0       
 [4] geneplotter_1.48.0   genefilter_1.52.1    futile.options_1.0.0
 [7] zlibbioc_1.16.0      lattice_0.20-33      RSQLite_1.0.0       
[10] foreign_0.8-66       xtable_1.8-2         gridExtra_2.2.1     
[13] plyr_1.8.3           tools_3.2.4          BiocParallel_1.4.3  
[16] annotate_1.48.0      lambda.r_1.1.7       XVector_0.10.0      
[19] futile.logger_1.4.1  scales_0.4.0         nnet_7.3-12         
[22] gtable_0.2.0         latticeExtra_0.6-28  cluster_2.0.3       
[25] rpart_4.1-10         munsell_0.4.3        grid_3.2.4          
[28] XML_3.98-1.4         colorspace_1.2-6     AnnotationDbi_1.32.3
[31] Hmisc_3.17-2         splines_3.2.4        survival_2.38-3     
[34] RColorBrewer_1.1-2   acepack_1.3-3.3      locfit_1.5-9.1  
QuasR • 2.4k views
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Entering edit mode
@martin-morgan-1513
Last seen 2 days ago
United States

The error indicates that you have a version of S4Vectors that is too old for the version of QuasR you are trying to install. This occurs because you are not following the supported way to install Bioconductor packages, which is

source("https://bioconductor.org/biocLite.R")
biocLite("QuasR")

If you are interested in using the 'devel' version of the package, then install the appropriate version of R (currently R-3.3.0). biocLite() will then install the correct version of S4Vectors, as well as the development version of QuasR.

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