Closed JianGuoZhou3 closed 4 years ago
Aufiero
commented
4 years ago Hi,
the file to use should be a file ending with .result so in your case should be clean.result See the package vignettes to see how to run circRNAprofiler and get expression from this file.
Best, S
JianGuoZhou3
commented
4 years ago Hi, so, I can remove others? I will try and feedback to you. Best,
Aufiero
commented
4 years ago I do not get your question. If you used only NCLscan you should have in your project folder named e.g. projectCirc only 1 subfolder named nclscan. Please follow the vignettes instructions. For example purpose a project folder named projectCirc was created in inst/extdata folder of the R package circRNAprofiler. You can have a look at it and modify that accordingly.
Best, S
JianGuoZhou3
commented
4 years ago for sure, I got it.
But now still have some errors.
I test nclscan and circexplorer2 independently.
however, there are errors.
# gtf <- formatGTF("gencode.V19.annotation.gtf")
gtf <- formatGTF("gencode.v34.annotation.gtf")
# For example purpose load a short version of the formatted gtf file generated
# using the command above.
data("gtf")
head(gtf)
save(gtf,file = "gencode.v34.hg38.gtf.Rdata")
> backSplicedJunctions <- getBackSplicedJunctions(gtf)
Error: Can't combine `..1$id` <logical> and `..2$id` <character>.
Run `rlang::last_error()` to see where the error occurred.There are my documents. Could you please help me to check those? Best, circexplorer2.zip nclscan.zip experiment.txt
Aufiero
commented
4 years ago Can you run sessionInfo() and send it to me? I want to see first if there is a problem with package versions.
JianGuoZhou3
commented
4 years ago > sessionInfo()R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] gridExtra_2.3
[2] VennDiagram_1.6.20
[3] futile.logger_1.4.3
[4] ggpubr_0.4.0
[5] ggplot2_3.3.2
[6] circRNAprofiler_1.0.0
[7] gwascat_2.18.0
[8] Homo.sapiens_1.3.1
[9] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[10] org.Hs.eg.db_3.10.0
[11] GO.db_3.10.0
[12] OrganismDbi_1.28.0
[13] GenomicFeatures_1.38.2
[14] GenomicRanges_1.38.0
[15] GenomeInfoDb_1.22.1
[16] AnnotationDbi_1.48.0
[17] IRanges_2.20.2
[18] S4Vectors_0.24.4
[19] Biobase_2.46.0
[20] BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.1.8
[3] Hmisc_4.4-1 AnnotationHub_2.18.0
[5] BiocFileCache_1.10.2 plyr_1.8.6
[7] splines_3.6.3 BiocParallel_1.20.1
[9] digest_0.6.25 htmltools_0.5.0
[11] magrittr_1.5 checkmate_2.0.0
[13] memoise_1.1.0 BSgenome_1.54.0
[15] cluster_2.1.0 openxlsx_4.1.5
[17] limma_3.42.2 Biostrings_2.54.0
[19] readr_1.3.1 annotate_1.64.0
[21] matrixStats_0.56.0 R.utils_2.9.2
[23] askpass_1.1 prettyunits_1.1.1
[25] jpeg_0.1-8.1 colorspace_1.4-1
[27] blob_1.2.1 rappdirs_0.3.1
[29] haven_2.3.1 xfun_0.16
[31] dplyr_1.0.1 crayon_1.3.4
[33] RCurl_1.98-1.2 graph_1.64.0
[35] genefilter_1.68.0 survival_3.2-3
[37] glue_1.4.1 gtable_0.3.0
[39] zlibbioc_1.32.0 XVector_0.26.0
[41] seqinr_3.6-1 DelayedArray_0.12.3
[43] car_3.0-9 abind_1.4-5
[45] scales_1.1.1 futile.options_1.0.1
[47] DBI_1.1.0 edgeR_3.28.1
[49] rstatix_0.6.0 Rcpp_1.0.5
[51] xtable_1.8-4 progress_1.2.2
[53] htmlTable_2.0.1 foreign_0.8-75
[55] bit_4.0.4 Formula_1.2-3
[57] htmlwidgets_1.5.1 httr_1.4.2
[59] RColorBrewer_1.1-2 ellipsis_0.3.1
[61] pkgconfig_2.0.3 XML_3.99-0.3
[63] R.methodsS3_1.8.0 nnet_7.3-14
[65] dbplyr_1.4.4 locfit_1.5-9.4
[67] tidyselect_1.1.0 rlang_0.4.7
[69] reshape2_1.4.4 later_1.1.0.1
[71] cellranger_1.1.0 munsell_0.5.0
[73] BiocVersion_3.10.1 tools_3.6.3
[75] generics_0.0.2 RSQLite_2.2.0
[77] ade4_1.7-15 broom_0.7.0
[79] stringr_1.4.0 fastmap_1.0.1
[81] yaml_2.2.1 knitr_1.29
[83] bit64_4.0.2 zip_2.1.0
[85] purrr_0.3.4 RBGL_1.62.1
[87] mime_0.9 formatR_1.7
[89] R.oo_1.23.0 biomaRt_2.42.1
[91] compiler_3.6.3 rstudioapi_0.11
[93] curl_4.3 png_0.1-7
[95] interactiveDisplayBase_1.24.0 ggsignif_0.6.0
[97] tibble_3.0.3 geneplotter_1.64.0
[99] stringi_1.4.6 forcats_0.5.0
[101] lattice_0.20-41 Matrix_1.2-18
[103] vctrs_0.3.2 pillar_1.4.6
[105] lifecycle_0.2.0 BiocManager_1.30.10
[107] data.table_1.12.8 bitops_1.0-6
[109] httpuv_1.5.4 rtracklayer_1.46.0
[111] R6_2.4.1 latticeExtra_0.6-29
[113] promises_1.1.1 rio_0.5.16
[115] lambda.r_1.2.4 MASS_7.3-51.6
[117] assertthat_0.2.1 SummarizedExperiment_1.16.1
[119] openssl_1.4.2 DESeq2_1.26.0
[121] withr_2.2.0 GenomicAlignments_1.22.1
[123] Rsamtools_2.2.3 GenomeInfoDbData_1.2.2
[125] hms_0.5.3 rpart_4.1-15
[127] tidyr_1.1.1 carData_3.0-4
[129] BSgenome.Hsapiens.UCSC.hg19_1.4.0 shiny_1.5.0
[131] base64enc_0.1-3
Aufiero
commented
4 years ago I see that you are the wrong version of circRNAprofiler. I suggest that you alway use BiocManager to install packages since it takes care of installing the package of interest and the correct versions of all the dependencies.
On the github page it is specified how to install circRNAprofiler.
Run 1) or 2).
1) You can install the release version (STABLE and recommended) of circRNAprofiler from Bioconductor using:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("circRNAprofiler")
To download the latest development version on github use:2) OR you can install the devel version (with some improvements) of circRNAprofiler from Bioconductor using:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("circRNAprofiler")Once you have done that you should not get any error.
Best, S
JianGuoZhou3
commented
4 years ago Hi, there are some errors.
library(circRNAprofiler)
Error: package or namespace load failed for ‘circRNAprofiler’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘ape’R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.> install.packages("ape")
There is a binary version available but the source version
is later:
binary source needs_compilation
ape 5.4 5.4-1 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y
installing the source package ‘ape’
trying URL 'https://cran.rstudio.com/src/contrib/ape_5.4-1.tar.gz'
Content type 'application/x-gzip' length 798605 bytes (779 KB)
==================================================
downloaded 779 KB
* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c BIONJ.c -o BIONJ.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c NNI.c -o NNI.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c SPR.c -o SPR.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c additive.c -o additive.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ape.c -o ape.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bNNI.c -o bNNI.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bionjs.c -o bionjs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bipartition.c -o bipartition.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bitsplits.c -o bitsplits.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c delta_plot.c -o delta_plot.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dist_dna.c -o dist_dna.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dist_nodes.c -o dist_nodes.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ewLasso.c -o ewLasso.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c heap.c -o heap.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mat_expo.c -o mat_expo.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c me.c -o me.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c me_balanced.c -o me_balanced.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c me_ols.c -o me_ols.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mvr.c -o mvr.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mvrs.c -o mvrs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nj.c -o nj.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c njs.c -o njs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pic.c -o pic.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c plot_phylo.c -o plot_phylo.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c prop_part.cpp -o prop_part.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rTrait.c -o rTrait.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c read_dna.c -o read_dna.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c reorder_Rcpp.cpp -o reorder_Rcpp.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c reorder_phylo.c -o reorder_phylo.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c treePop.c -o treePop.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c tree_build.c -o tree_build.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c tree_phylo.c -o tree_phylo.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c triangMtd.c -o triangMtd.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c triangMtds.c -o triangMtds.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ultrametric.c -o ultrametric.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [ape.so] Error 1
ERROR: compilation failed for package ‘ape’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ape’
Warning in install.packages :
installation of package ‘ape’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/h1/wph5l7kn6sq020007z1bq2d00000gn/T/RtmpSZFWW3/downloaded_packages’
Do you have any method to solve this? Best,
Aufiero
commented
4 years ago Hi,
I can not reproduce the error.
-Try to close everything, R or R studio, and install the ape package using BiocManager.
-An alternative you can reset everything so this means that you can delete all the packages in the user R library folder 4.0 that usually is e.g. your user/R/win-library and run again:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("circRNAprofiler")This command should install all the required packages.
After you have done that can you run sessionInfo() and post it here?
Best, S
JianGuoZhou3
commented
4 years ago Hi Thanks, After deleting all of R and related documents, and re-install this package. Now, it works, and very convenient. Best,
I used NCLscan
After run,
But, I don't know keep which docunments and input to circRNAprofiler. Best,