rm message, add dplyr

pdimens · Jul 19, 2024 · 74f6c40 · 74f6c40
1 parent f2b379a
commit 74f6c40
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Showing 14 changed files with 2 additions and 16 deletions.
diff --git a/src/harpy/conda_deps.py b/src/harpy/conda_deps.py
@@ -30,6 +30,7 @@ def generate_conda_deps():
             ],
         "r" : [
             "conda-forge::r-dt",
+            "conda-forge::r-dplyr",
             "conda-forge::r-flexdashboard",
             "conda-forge::r-ggplot2",
             "conda-forge::r-highcharter",

diff --git a/src/harpy/reports/AlignBxStats.Rmd b/src/harpy/reports/AlignBxStats.Rmd
@@ -21,7 +21,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/AlignStats.Rmd b/src/harpy/reports/AlignStats.Rmd
@@ -23,7 +23,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/BcftoolsStats.Rmd b/src/harpy/reports/BcftoolsStats.Rmd
@@ -21,7 +21,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/BxCount.Rmd b/src/harpy/reports/BxCount.Rmd
@@ -20,7 +20,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/HapCut2.Rmd b/src/harpy/reports/HapCut2.Rmd
@@ -21,7 +21,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/Impute.Rmd b/src/harpy/reports/Impute.Rmd
@@ -22,7 +22,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/Leviathan.Rmd b/src/harpy/reports/Leviathan.Rmd
@@ -20,7 +20,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/LeviathanPop.Rmd b/src/harpy/reports/LeviathanPop.Rmd
@@ -20,7 +20,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/Naibr.Rmd b/src/harpy/reports/Naibr.Rmd
@@ -50,7 +50,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/NaibrPop.Rmd b/src/harpy/reports/NaibrPop.Rmd
@@ -22,7 +22,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/PreflightBam.Rmd b/src/harpy/reports/PreflightBam.Rmd
@@ -20,7 +20,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/PreflightFastq.Rmd b/src/harpy/reports/PreflightFastq.Rmd
@@ -14,15 +14,12 @@ output:
       - { title : "Source", icon: "fa-github", href: "https://www.github.com/pdimens/harpy/", align: right }
 ---
 
-```{r load environment, echo=FALSE, message=TRUE, warning=FALSE}
+```{r load environment, echo=FALSE, message=FALSE, warning=FALSE}
 using<-function(...) {
     libs<-unlist(list(...))
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
-        cat(paste("Installing:", need))
-        message(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }

diff --git a/src/harpy/reports/StitchCollate.Rmd b/src/harpy/reports/StitchCollate.Rmd
@@ -42,7 +42,6 @@ using<-function(...) {
     req<-unlist(lapply(libs,require,character.only=TRUE))
     need<-libs[req==FALSE]
     if(length(need)>0){ 
-        print(paste("Installing:", need))
         install.packages(need, repos = "https://cloud.r-project.org/")
         lapply(need,require,character.only=TRUE)
     }