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
Hi,
I tried to run the first example from the vignettes
BatchQC ExamplesI got the error like:
My running environment is: