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hyunhwan-jeong / CB2

CB2 is an R package which provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
https://cran.r-project.org/web/packages/CB2/index.html
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run_sgrna_quant not found #2

Closed mroorda closed 4 years ago

mroorda commented 5 years ago

Unfortunately, when I try and follow the tutorial available from CRAN, the function run_sgrna_quant was not found. Could you resolve this issue?

hyunhwan-jeong commented 5 years ago

@mroorda,

Can you share the error message and outputs of sessionInfo()?

Thank you,

Hyun-Hwan Jeong

mroorda commented 5 years ago

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"

hyunhwan-jeong commented 5 years ago

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)
hyunhwan-jeong commented 5 years ago

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
hyunhwan-jeong commented 5 years ago

@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)
mroorda commented 5 years ago

@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.

hyunhwan-jeong commented 5 years ago

Good to hear that, @mroorda!

Did you install CB2 using devtools before?

mroorda commented 5 years ago

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

** 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

include 

                    ^

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'

hyunhwan-jeong commented 5 years ago

@mroorda thanks for the detailed report!

I will try to reproduce the error and will find a solution.

Kind Regards,

Hyun-Hwan Jeong