From 8296ab68fe44f7f7511d4d7e488678c63257b2cb Mon Sep 17 00:00:00 2001
From: WortJohn <1004794592@qq.com>
Date: Tue, 17 Dec 2024 20:53:32 +0800
Subject: [PATCH 1/7] Update gcstats.R read.R and MD5 files
the "chunk.apply" function from R iotools package does not have "parallel" parameter which has been changed to "CH.PARALLEL"
---
R/gcstats.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/R/gcstats.R b/R/gcstats.R
index 9c7b0fa..c6a5e1b 100644
--- a/R/gcstats.R
+++ b/R/gcstats.R
@@ -22,7 +22,7 @@ gc.sample.stats <- function(file, col_types = "c--dd----d----",
message("Collecting GC information ", appendLF = FALSE)
}
res <- chunk.apply(input = con, FUN = parse_chunck, col_types = col_types,
- CH.MAX.SIZE = buffer, parallel = parallel)
+ CH.MAX.SIZE = buffer, CH.PARALLEL = parallel)
close(con)
if (verbose){
message(" done\n")
From df12a278bf3bd05fb6e0672bac7df91e27772f5f Mon Sep 17 00:00:00 2001
From: WortJohn <1004794592@qq.com>
Date: Tue, 17 Dec 2024 20:57:53 +0800
Subject: [PATCH 2/7] Update gcstats.R read.R and MD5 files
the "chunk.apply" function from R iotools package does not have "parallel" parameter which has been changed to "CH.PARALLEL"
---
R/read.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/R/read.R b/R/read.R
index 6de1968..11e120a 100644
--- a/R/read.R
+++ b/R/read.R
@@ -43,7 +43,7 @@ read.seqz.chr <- function(file, chr_name, col_names,
}
res <- chunk.apply(input = con, FUN = parse_chunck, chr_name = chr_name,
col_names = col_names, col_types = col_types, CH.MAX.SIZE = buffer,
- parallel = parallel)
+ CH.PARALLEL = parallel)
close(con)
res
}
From 59d840ccf6177bb794b8d059a28d7ec13da80e39 Mon Sep 17 00:00:00 2001
From: WortJohn <1004794592@qq.com>
Date: Tue, 17 Dec 2024 21:00:20 +0800
Subject: [PATCH 3/7] Update gcstats.R read.R and MD5 files
the "chunk.apply" function from R iotools package does not have "parallel" parameter which has been changed to "CH.PARALLEL"
---
MD5 | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/MD5 b/MD5
index afc4752..a2d3769 100644
--- a/MD5
+++ b/MD5
@@ -4,12 +4,12 @@ dc74f3941cd7eb5d5d2820a78e855291 *NEWS
0090c3e305006e38f8ec8cef5616a3e2 *R/bayes.R
1c95cfc1a6597466e42c386b0c6a6196 *R/extract.R
c37085ee8b851dfd42eea66341904e82 *R/fit.R
-06b55a573555d6e0315478fb47fd48c0 *R/gcstats.R
+594c9ccd9c0816666791fb018756c2b2 *R/gcstats.R
3ad97d0891d98e23cd5be6b4417067c5 *R/graphics.R
79624c9cf668bfb2b05e8a339e98f393 *R/misc.R
4b7f3320bad5b252cc0727ba9e019ab8 *R/model.R
8ab48098af7628c6d2f155b8f9f24b74 *R/mutations.R
-1415cb2b3e892624fb7ea4ff76a2c46f *R/read.R
+574485fa2da5de558b74b117512a84a7 *R/read.R
bfe91a98d0c94dab8ae8bcb554eb5acd *R/results.R
f763a946f45e700642201c486263b969 *R/segments.R
0359f75dbcc67975a0a8654cc04e32a3 *R/solutions.R
From 8bd3ac8baac3caaae000a76b53ef9487a3d02a73 Mon Sep 17 00:00:00 2001
From: WortJohn <1004794592@qq.com>
Date: Tue, 17 Dec 2024 21:28:30 +0800
Subject: [PATCH 4/7] Create README.md
---
README.md | 7 +++++++
1 file changed, 7 insertions(+)
create mode 100644 README.md
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..83301ac
--- /dev/null
+++ b/README.md
@@ -0,0 +1,7 @@
+Solve the following issues:
+Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)
+Calls: main ... preprocess.seqz -> sequenza.extract -> gc.sample.stats -> chunk.apply
+Execution halted
+
+The reason:
+The "chunk.apply" function from R iotools package with new version does not have "parallel" parameter which has been changed to "CH.PARALLEL"
From b46aa6d635b0d5610f14851ac18a45a09a791335 Mon Sep 17 00:00:00 2001
From: WortJohn <1004794592@qq.com>
Date: Tue, 17 Dec 2024 21:29:10 +0800
Subject: [PATCH 5/7] Update README.md
---
README.md | 2 ++
1 file changed, 2 insertions(+)
diff --git a/README.md b/README.md
index 83301ac..f6a508a 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,9 @@
Solve the following issues:
+-
Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)
Calls: main ... preprocess.seqz -> sequenza.extract -> gc.sample.stats -> chunk.apply
Execution halted
The reason:
+-
The "chunk.apply" function from R iotools package with new version does not have "parallel" parameter which has been changed to "CH.PARALLEL"
From 28c12d0e9e67ae3449cf359ad9e66ea55bb575ae Mon Sep 17 00:00:00 2001
From: WortJohn <1004794592@qq.com>
Date: Tue, 17 Dec 2024 21:29:56 +0800
Subject: [PATCH 6/7] Update README.md
---
README.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index f6a508a..8b68a46 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,9 @@
Solve the following issues:
--
+
Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)
Calls: main ... preprocess.seqz -> sequenza.extract -> gc.sample.stats -> chunk.apply
Execution halted
The reason:
--
+
The "chunk.apply" function from R iotools package with new version does not have "parallel" parameter which has been changed to "CH.PARALLEL"
From ccb9983b9617b6d2176c972cd8506a81d69701e1 Mon Sep 17 00:00:00 2001
From: WortJohn <1004794592@qq.com>
Date: Wed, 18 Dec 2024 08:57:53 +0800
Subject: [PATCH 7/7] Update README.md
---
README.md | 2 ++
1 file changed, 2 insertions(+)
diff --git a/README.md b/README.md
index 8b68a46..afd1914 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,9 @@
Solve the following issues:
Collecting GC information Error in (function (x, col_types) : unused argument (parallel = 1)
+
Calls: main ... preprocess.seqz -> sequenza.extract -> gc.sample.stats -> chunk.apply
+
Execution halted
The reason: