Running errors

[YulongNiu]

Hi,

I tried to run the first example from the vignettes BatchQC Examples

library(BatchQC)
nbatch <- 3
ncond <- 2
npercond <- 10
data.matrix <- rnaseq_sim(ngenes=50, nbatch=nbatch, ncond=ncond, npercond=
    npercond, basemean=10000, ggstep=50, bbstep=2000, ccstep=800, 
    basedisp=100, bdispstep=-10, swvar=1000, seed=1234)
batch <- rep(1:nbatch, each=ncond*npercond)
condition <- rep(rep(1:ncond, each=npercond), nbatch)
batchQC(data.matrix, batch=batch, condition=condition, 
        report_file="batchqc_report.html", report_dir=".", 
        report_option_binary="111111111",
        view_report=FALSE, interactive=TRUE, batchqc_output=TRUE)

I got the error like:

Error in file(con, "w") : cannot open the connection
In addition: Warning message:
In file(con, "w") :
  cannot open file 'batchqc_report.knit.md': Permission denied

My running environment is:

R version 3.6.1 (2019-07-05)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 31 (Thirty One)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets 
[6] methods   base     

other attached packages:
[1] BatchQC_1.13.1

loaded via a namespace (and not attached):
 [1] Biobase_2.44.0       splines_3.6.1       
 [3] bit64_0.9-7          gtools_3.8.1        
 [5] shiny_1.4.0          moments_0.14        
 [7] assertthat_0.2.1     stats4_3.6.1        
 [9] pander_0.6.3         blob_1.2.0          
[11] yaml_2.2.0           backports_1.1.5     
[13] pillar_1.4.2         RSQLite_2.1.2       
[15] lattice_0.20-38      quantreg_5.51       
[17] glue_1.3.1           limma_3.40.6        
[19] digest_0.6.22        promises_1.1.0      
[21] htmltools_0.4.0      httpuv_1.5.2        
[23] Matrix_1.2-17        plyr_1.8.4          
[25] XML_3.98-1.20        pkgconfig_2.0.3     
[27] SparseM_1.77         genefilter_1.66.0   
[29] purrr_0.3.3          xtable_1.8-4        
[31] corpcor_1.6.9        gdata_2.18.0        
[33] later_1.0.0          BiocParallel_1.18.1 
[35] MatrixModels_0.4-1   tibble_2.1.3        
[37] annotate_1.62.0      mgcv_1.8-30         
[39] IRanges_2.18.3       ggvis_0.4.5         
[41] BiocGenerics_0.30.0  survival_3.1-6      
[43] magrittr_1.5         crayon_1.3.4        
[45] mime_0.7             memoise_1.1.0       
[47] mcmc_0.9-6           evaluate_0.14       
[49] nlme_3.1-141         MASS_7.3-51.4       
[51] gplots_3.0.1.1       tools_3.6.1         
[53] matrixStats_0.55.0   stringr_1.4.0       
[55] MCMCpack_1.4-4       S4Vectors_0.22.1    
[57] AnnotationDbi_1.46.1 compiler_3.6.1      
[59] caTools_1.17.1.2     rlang_0.4.1         
[61] grid_3.6.1           RCurl_1.95-4.12     
[63] rstudioapi_0.10      htmlwidgets_1.5.1   
[65] bitops_1.0-6         base64enc_0.1-3     
[67] rmarkdown_1.16       d3heatmap_0.6.1.2   
[69] DBI_1.0.0            reshape2_1.4.3      
[71] R6_2.4.0             knitr_1.25          
[73] dplyr_0.8.3          fastmap_1.0.1       
[75] bit_1.1-14           zeallot_0.1.0       
[77] KernSmooth_2.23-16   stringi_1.4.3       
[79] parallel_3.6.1       sva_3.32.1          
[81] Rcpp_1.0.2           vctrs_0.2.0         
[83] png_0.1-7            tidyselect_0.2.5    
[85] xfun_0.10            coda_0.19-3  

[mani2012]

Hi, Please make sure that the directory from where you are running or the ‘report_dir’ option that you are passing is writable. Best, Mani From: Yulong Niu <notifications@github.com> Sent: Wednesday, November 6, 2019 12:34 PM To: mani2012/BatchQC <BatchQC@noreply.github.com> Cc: Subscribed <subscribed@noreply.github.com> Subject: [mani2012/BatchQC] Running errors (#14) Hi, I tried to run the first example from the vignettes BatchQC Examples library(BatchQC) nbatch <- 3 ncond <- 2 npercond <- 10 data.matrix <- rnaseq_sim(ngenes=50, nbatch=nbatch, ncond=ncond, npercond= npercond, basemean=10000, ggstep=50, bbstep=2000, ccstep=800, basedisp=100, bdispstep=-10, swvar=1000, seed=1234) batch <- rep(1:nbatch, each=ncond*npercond) condition <- rep(rep(1:ncond, each=npercond), nbatch) batchQC(data.matrix, batch=batch, condition=condition, report_file="batchqc_report.html", report_dir=".", report_option_binary="111111111", view_report=FALSE, interactive=TRUE, batchqc_output=TRUE) I got the error like: Error in file(con, "w") : cannot open the connection In addition: Warning message: In file(con, "w") : cannot open file 'batchqc_report.knit.md': Permission denied My running environment is: R version 3.6.1 (2019-07-05) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Fedora 31 (Thirty One) Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets [6] methods base other attached packages: [1] BatchQC_1.13.1 loaded via a namespace (and not attached): [1] Biobase_2.44.0 splines_3.6.1 [3] bit64_0.9-7 gtools_3.8.1 [5] shiny_1.4.0 moments_0.14 [7] assertthat_0.2.1 stats4_3.6.1 [9] pander_0.6.3 blob_1.2.0 [11] yaml_2.2.0 backports_1.1.5 [13] pillar_1.4.2 RSQLite_2.1.2 [15] lattice_0.20-38 quantreg_5.51 [17] glue_1.3.1 limma_3.40.6 [19] digest_0.6.22 promises_1.1.0 [21] htmltools_0.4.0 httpuv_1.5.2 [23] Matrix_1.2-17 plyr_1.8.4 [25] XML_3.98-1.20 pkgconfig_2.0.3 [27] SparseM_1.77 genefilter_1.66.0 [29] purrr_0.3.3 xtable_1.8-4 [31] corpcor_1.6.9 gdata_2.18.0 [33] later_1.0.0 BiocParallel_1.18.1 [35] MatrixModels_0.4-1 tibble_2.1.3 [37] annotate_1.62.0 mgcv_1.8-30 [39] IRanges_2.18.3 ggvis_0.4.5 [41] BiocGenerics_0.30.0 survival_3.1-6 [43] magrittr_1.5 crayon_1.3.4 [45] mime_0.7 memoise_1.1.0 [47] mcmc_0.9-6 evaluate_0.14 [49] nlme_3.1-141 MASS_7.3-51.4 [51] gplots_3.0.1.1 tools_3.6.1 [53] matrixStats_0.55.0 stringr_1.4.0 [55] MCMCpack_1.4-4 S4Vectors_0.22.1 [57] AnnotationDbi_1.46.1 compiler_3.6.1 [59] caTools_1.17.1.2 rlang_0.4.1 [61] grid_3.6.1 RCurl_1.95-4.12 [63] rstudioapi_0.10 htmlwidgets_1.5.1 [65] bitops_1.0-6 base64enc_0.1-3 [67] rmarkdown_1.16 d3heatmap_0.6.1.2 [69] DBI_1.0.0 reshape2_1.4.3 [71] R6_2.4.0 knitr_1.25 [73] dplyr_0.8.3 fastmap_1.0.1 [75] bit_1.1-14 zeallot_0.1.0 [77] KernSmooth_2.23-16 stringi_1.4.3 [79] parallel_3.6.1 sva_3.32.1 [81] Rcpp_1.0.2 vctrs_0.2.0 [83] png_0.1-7 tidyselect_0.2.5 [85] xfun_0.10 coda_0.19-3 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#14?email_source=notifications&email_token=ACMB4PGUNA4BHQT4IKJSWKTQSL5W3A5CNFSM4JJYZTB2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HXJR6MQ>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACMB4PE4EVOKQVDT4YEJRPDQSL5W3ANCNFSM4JJYZTBQ>.