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mani2012 / BatchQC

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.
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Running errors #14

Open YulongNiu opened 5 years ago

YulongNiu commented 5 years ago

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 commented 5 years ago

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

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