Closed mroorda closed 4 years ago
@mroorda,
Can you share the error message and outputs of sessionInfo()
?
Thank you,
Hyun-Hwan Jeong
R version 3.5.3 (2019-03-11) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale: [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 LC_MONETARY=Dutch_Netherlands.1252 [4] LC_NUMERIC=C LC_TIME=Dutch_Netherlands.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] CB2_1.1 ggplot2_3.1.1 dplyr_0.8.0.1 tibble_2.1.1 glue_1.3.1 magrittr_1.5
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 rstudioapi_0.10 tidyselect_0.2.5 munsell_0.5.0 colorspace_1.4-1 R6_2.4.0 rlang_0.3.4
[8] fansi_0.4.0 plyr_1.8.4 tools_3.5.3 grid_3.5.3 gtable_0.3.0 utf8_1.1.4 cli_1.1.0
[15] withr_2.1.2 yaml_2.2.0 lazyeval_0.2.2 assertthat_0.2.1 crayon_1.3.4 RColorBrewer_1.1-2 purrr_0.3.2
[22] pheatmap_1.0.12 compiler_3.5.3 pillar_1.3.1 scales_1.0.0 pkgconfig_2.0.2
cb2_count <- run_sgrna_quant(FASTA, df_design) Error in run_sgrna_quant(FASTA, df_design) : could not find function "run_sgrna_quant"
I am still figuring out what the problem is. Do you see the same error if you run the following line?
cb2_count <- CB2::run_sgrna_quant(FASTA, df_design)
I suspect OS (windows) can be an issue, but I can't replicate the same error in my windows machine.
> cb2_count <- run_sgrna_quant(FASTA, df_design)
Detects the length of guided RNA is 20
25 gRNAs were found from the gRNA_Reference library.
All 688 were proceed!
Detects the length of guided RNA is 20
25 gRNAs were found from the gRNA_Reference library.
All 608 were proceed!
Detects the length of guided RNA is 20
25 gRNAs were found from the gRNA_Reference library.
All 703 were proceed!
Detects the length of guided RNA is 20
25 gRNAs were found from the gRNA_Reference library.
All 659 were proceed!
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.1.1 dplyr_0.8.0.1 tibble_2.1.1 glue_1.3.1 magrittr_1.5 CB2_1.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 tidyselect_0.2.5 munsell_0.5.0 colorspace_1.4-1 R6_2.4.0 rlang_0.3.4 fansi_0.4.0 plyr_1.8.4 tools_3.5.3 grid_3.5.3 gtable_0.3.0 utf8_1.1.4
[13] cli_1.1.0 withr_2.1.2 lazyeval_0.2.2 assertthat_0.2.1 crayon_1.3.4 purrr_0.3.2 RColorBrewer_1.1-2 pheatmap_1.0.12 compiler_3.5.3 pillar_1.3.1 scales_1.0.0 pkgconfig_2.0.2
@mroorda, Can you see the same thing when you run lsf.str("package:CB2")
?
> lsf.str("package:CB2")
calc_mappability : function (count_obj, df_design)
fit_ab : function (xvec, nvec)
get_CPM : function (sgcount)
measure_gene_stats : function (sgrna_stat)
plot_corr_heatmap : function (sgcount, df_design, cor_method = "pearson")
plot_count_distribution : function (sgcount, df_design)
plot_dotplot : function (sgcount, df_design, gene)
plot_PCA : function (sgcount, df_design)
quant : function (ref_path, fastq_path)
run_estimation : function (sgcount, design, group_a, group_b)
run_sgrna_quant : function (lib_path, design)
@hyunhwaj Thanks for the swift efforts to resolve this issue! I reinstalled the package from CRAN, and miraculously, the example script ran without any problems.
Good to hear that, @mroorda!
Did you install CB2 using devtools
before?
Good to hear that, @mroorda!
Did you install CB2 using
devtools
before?
@hyunhwaj no that was not necessary, installing from CRAN was sufficient! But just for the record, when I try installing CB2 using devtools, compilation fails for package 'RcppArmadillo' (see error below). For now, I can use CB2 from CRAN, but for people who want to install from this repo, I can imagine you might want to look into this. So FYI:
`> devtools::install_github("hyunhwaj/CB2") Downloading GitHub repo hyunhwaj/CB2@master These packages have more recent versions available. Which would you like to update?
1: RcppArmad... (0.9.300.2.0 -> 0.9.400.2.0) [CRAN]
Enter one or more numbers separated by spaces, or an empty line to cancel 1: 1 RcppArmad... (0.9.300.2.0 -> 0.9.400.2.0) [CRAN] Installing 1 packages: RcppArmadillo Installing package into ‘\zkh/dfs/Gebruikers19/RoordaM/Data/R/win-library/3.5’ (as ‘lib’ is unspecified)
There is a binary version available but the source version is later: binary source needs_compilation RcppArmadillo 0.9.300.2.0 0.9.400.2.0 TRUE
installing the source package ‘RcppArmadillo’
trying URL 'https://cran.rstudio.com/src/contrib/RcppArmadillo_0.9.400.2.0.tar.gz' Content type 'application/x-gzip' length 1348025 bytes (1.3 MB) downloaded 1.3 MB
installing source package 'RcppArmadillo' ... ** package 'RcppArmadillo' successfully unpacked and MD5 sums checked
WARNING: this package has a configure script It probably needs manual configuration
** libs C:/RBuildTools/3.5/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-35~1.3/include" -DNDEBUG -I"\zkh/dfs/Gebruikers19/RoordaM/Data/R/win-library/3.5/Rcpp/include" -I../inst/include -I. -fopenmp -O2 -Wall -mtune=generic -c RcppArmadillo.cpp -o RcppArmadillo.o In file included from ../inst/include/RcppArmadillo.h:31:0, from RcppArmadillo.cpp:22: ../inst/include/RcppArmadilloForward.h:26:24: fatal error: RcppCommon.h: No such file or directory
^
compilation terminated. make: *** [C:/PROGRA~1/R/R-35~1.3/etc/x64/Makeconf:215: RcppArmadillo.o] Error 1 ERROR: compilation failed for package 'RcppArmadillo'
@mroorda thanks for the detailed report!
I will try to reproduce the error and will find a solution.
Kind Regards,
Hyun-Hwan Jeong
Unfortunately, when I try and follow the tutorial available from CRAN, the function
run_sgrna_quant
was not found. Could you resolve this issue?